{"text_format":"3","workbook":"xlsx","n_sheets":10,"sheets":["01TL","02DF","04HS","05PG","06BH","08DJ","09JM","10LD","11JZ","12GW"],"not_rendered":{"defined_names":10},"read":"whole","date_system":"1900"}

{"sheet":"01TL","index":0,"n_rows":638,"n_cols":107,"rows_kept":638}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","A2M","chr12:9099443","A2M(P547S)",null,null,"disulfide bond ",{"$nulls":3},127,"PASS","Missense","rs1188354164",-1,null,"FUNCTION: Is able to inhibit all four classes of proteinases by a unique 'trapping' mechanism. This protein has a peptide stretch, called the 'bait region' which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein which traps the proteinase. The entrapped enzyme remains active against low molecular weight substrates (activity against high molecular weight substrates is greatly reduced). Following cleavage in the bait region, a thioester bond is hydrolyzed and mediates the covalent binding of the protein to the proteinase.; ",{"$nulls":4},"p.Pro547Ser","c.1639C>T","MODERATE","547/1474",14,{"$nulls":5},"1",{"$nulls":30},"3.154183","-0.26","3.095","0.998499","-7.18","0.99","0.02","0.212",{"$nulls":3},"Unknown",-1,"AD","Alpha-2-macroglobulin deficiency","General",{"$nulls":3},"C0002395","0/0","255,0","0","256","0/1","204,11","0.0512","215",null,"chr12:9099443:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0512"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ABCB4","chr7:87462868","ABCB4(L59Q)",null,null,"transmembrane region (Helical ), domain (ABC transmembrane type-1 1 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cholestasis, progressive familial intrahepatic, 3 (PFIC3) [MIM:602347]: A disorder characterized by early onset of cholestasis that progresses to hepatic fibrosis, cirrhosis, and end-stage liver disease before adulthood. {ECO:0000269|PubMed:11313315, ECO:0000269|PubMed:12671900, ECO:0000269|PubMed:17726488, ECO:0000269|PubMed:21119540, ECO:0000269|PubMed:24045840, ECO:0000269|PubMed:24594635, ECO:0000269|PubMed:24806754, ECO:0000269|PubMed:28012258, ECO:0000269|PubMed:9419367}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cholestasis of pregnancy, intrahepatic 3 (ICP3) [MIM:614972]: A liver disorder of pregnancy. It presents during the second or, more commonly, the third trimester of pregnancy with intense pruritus which becomes more severe with advancing gestation and cholestasis. It causes fetal distress, spontaneous premature delivery and intrauterine death. Patients have spontaneous and progressive disappearance of cholestasis after delivery. Cholestasis results from abnormal biliary transport from the liver into the small intestine. {ECO:0000269|PubMed:10767346, ECO:0000269|PubMed:12746424, ECO:0000269|PubMed:15077010}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Gallbladder disease 1 (GBD1) [MIM:600803]: One of the major digestive diseases. Gallstones composed of cholesterol (cholelithiasis) are the common manifestations in western countries. Most people with gallstones, however, remain asymptomatic through their lifetimes. {ECO:0000269|PubMed:11313316, ECO:0000269|PubMed:12891548, ECO:0000269|PubMed:22331132, ECO:0000269|PubMed:23533021, ECO:0000269|PubMed:24723470, ECO:0000269|PubMed:28012258, ECO:0000269|Ref.2}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Energy-dependent phospholipid efflux translocator that acts as a positive regulator of biliary lipid secretion. Functions as a floppase that translocates specifically phosphatidylcholine (PC) from the inner to the outer leaflet of the canalicular membrane bilayer into the canaliculi of hepatocytes. Translocation of PC makes the biliary phospholipids available for extraction into the canaliculi lumen by bile salt mixed micelles and therefore protects the biliary tree from the detergent activity of bile salts (PubMed:7957936, PubMed:8898203, PubMed:9366571, PubMed:17523162, PubMed:23468132, PubMed:24806754, PubMed:24723470, PubMed:24594635, PubMed:21820390). Plays a role in the recruitment of phosphatidylcholine (PC), phosphatidylethanolamine (PE) and sphingomyelin (SM) molecules to nonraft membranes and to fu rther enrichment of SM and cholesterol in raft membranes in hepatocytes (PubMed:23468132). Required for proper phospholipid bile formation (By similarity). Indirectly involved in cholesterol efflux activity from hepatocytes into the canalicular lumen in the presence of bile salts in an ATP- dependent manner (PubMed:24045840). Promotes biliary phospholipid secretion as canaliculi-containing vesicles from the canalicular plasma membrane (PubMed:9366571, PubMed:28012258). In cooperation with ATP8B1, functions to protect hepatocytes from the deleterious detergent activity of bile salts (PubMed:21820390). Does not confer multidrug resistance (By similarity). {ECO:0000250|UniProtKB:P21440, ECO:0000269|PubMed:17523162, ECO:0000269|PubMed:21820390, ECO:0000269|PubMed:23468132, ECO:0000269|PubMed:24045840, ECO:0000269|PubMed:24594635, ECO:0000269|PubMed:24723470, ECO:0000269|PubMed:24806754, ECO:0000269|PubMed:28012258, ECO:0000269|PubMed:7957936, ECO:0000269|PubMed:8898203, ECO:0000269|PubMed:9366571}.; ",{"$nulls":4},"p.Leu59Gln","c.176T>A","MODERATE","59/1286",4,{"$nulls":5},"5","560","525","369","332","501","480","0","0","0","0.1583",{"$nulls":20},"3.8131209999999998",".;-1.58;-1.58;-1.58;-1.58;.","3.56;3.56;3.56;3.56;3.56;.","0.999914",".;-3.59;-3.56;-3.56;-3.59;-4.91","0.959;.;0.967;0.959;.;.",".;0.007;0.005;0.005;0.007;0.002",".;0.528;0.552;0.534;0.528;.",{"$nulls":3},"Unknown",-1,"AD/AR","Cholestasis, progressive familial intrahepatic 3; Low phospholipid-associated cholelithiasis 1;  Cholestasis, oral contraceptives induced; Cholestasis, familial intrahepatic, of pregnancy; Gallbladder disease 1","Gastrointestinal",{"$nulls":3},"C3554241| C2609268| C1865643","0/0","531,0","0","531","0/1","425,84","0.165","509",null,"chr7:87462868:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1596"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ABCB4","chr7:87462868","ABCB4(L59Q)",null,null,"transmembrane region (Helical ), domain (ABC transmembrane type-1 1 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cholestasis, progressive familial intrahepatic, 3 (PFIC3) [MIM:602347]: A disorder characterized by early onset of cholestasis that progresses to hepatic fibrosis, cirrhosis, and end-stage liver disease before adulthood. {ECO:0000269|PubMed:11313315, ECO:0000269|PubMed:12671900, ECO:0000269|PubMed:17726488, ECO:0000269|PubMed:21119540, ECO:0000269|PubMed:24045840, ECO:0000269|PubMed:24594635, ECO:0000269|PubMed:24806754, ECO:0000269|PubMed:28012258, ECO:0000269|PubMed:9419367}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cholestasis of pregnancy, intrahepatic 3 (ICP3) [MIM:614972]: A liver disorder of pregnancy. It presents during the second or, more commonly, the third trimester of pregnancy with intense pruritus which becomes more severe with advancing gestation and cholestasis. It causes fetal distress, spontaneous premature delivery and intrauterine death. Patients have spontaneous and progressive disappearance of cholestasis after delivery. Cholestasis results from abnormal biliary transport from the liver into the small intestine. {ECO:0000269|PubMed:10767346, ECO:0000269|PubMed:12746424, ECO:0000269|PubMed:15077010}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Gallbladder disease 1 (GBD1) [MIM:600803]: One of the major digestive diseases. Gallstones composed of cholesterol (cholelithiasis) are the common manifestations in western countries. Most people with gallstones, however, remain asymptomatic through their lifetimes. {ECO:0000269|PubMed:11313316, ECO:0000269|PubMed:12891548, ECO:0000269|PubMed:22331132, ECO:0000269|PubMed:23533021, ECO:0000269|PubMed:24723470, ECO:0000269|PubMed:28012258, ECO:0000269|Ref.2}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Energy-dependent phospholipid efflux translocator that acts as a positive regulator of biliary lipid secretion. Functions as a floppase that translocates specifically phosphatidylcholine (PC) from the inner to the outer leaflet of the canalicular membrane bilayer into the canaliculi of hepatocytes. Translocation of PC makes the biliary phospholipids available for extraction into the canaliculi lumen by bile salt mixed micelles and therefore protects the biliary tree from the detergent activity of bile salts (PubMed:7957936, PubMed:8898203, PubMed:9366571, PubMed:17523162, PubMed:23468132, PubMed:24806754, PubMed:24723470, PubMed:24594635, PubMed:21820390). Plays a role in the recruitment of phosphatidylcholine (PC), phosphatidylethanolamine (PE) and sphingomyelin (SM) molecules to nonraft membranes and to fu rther enrichment of SM and cholesterol in raft membranes in hepatocytes (PubMed:23468132). Required for proper phospholipid bile formation (By similarity). Indirectly involved in cholesterol efflux activity from hepatocytes into the canalicular lumen in the presence of bile salts in an ATP- dependent manner (PubMed:24045840). Promotes biliary phospholipid secretion as canaliculi-containing vesicles from the canalicular plasma membrane (PubMed:9366571, PubMed:28012258). In cooperation with ATP8B1, functions to protect hepatocytes from the deleterious detergent activity of bile salts (PubMed:21820390). Does not confer multidrug resistance (By similarity). {ECO:0000250|UniProtKB:P21440, ECO:0000269|PubMed:17523162, ECO:0000269|PubMed:21820390, ECO:0000269|PubMed:23468132, ECO:0000269|PubMed:24045840, ECO:0000269|PubMed:24594635, ECO:0000269|PubMed:24723470, ECO:0000269|PubMed:24806754, ECO:0000269|PubMed:28012258, ECO:0000269|PubMed:7957936, ECO:0000269|PubMed:8898203, ECO:0000269|PubMed:9366571}.; ",{"$nulls":4},"p.Leu59Gln","c.176T>A","MODERATE","59/1286",4,{"$nulls":5},"5","560","562","369","356","501","509","0","0","0","0.0589",{"$nulls":20},"3.8131209999999998",".;-1.58;-1.58;-1.58;-1.58;.","3.56;3.56;3.56;3.56;3.56;.","0.999914",".;-3.59;-3.56;-3.56;-3.59;-4.91","0.959;.;0.967;0.959;.;.",".;0.007;0.005;0.005;0.007;0.002",".;0.528;0.552;0.534;0.528;.",{"$nulls":3},"Unknown",-1,"AD/AR","Cholestasis, progressive familial intrahepatic 3; Low phospholipid-associated cholelithiasis 1;  Cholestasis, oral contraceptives induced; Cholestasis, familial intrahepatic, of pregnancy; Gallbladder disease 1","Gastrointestinal",{"$nulls":3},"C3554241| C2609268| C1865643","0/0","531,0","0","531","0/1","508,34","0.0627","542",null,"chr7:87462868:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0674"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ABCC9","chr12:21844496","ABCC9(N1101S)",null,null,"topological domain (Cytoplasmic ), domain (ABC transmembrane type-1 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cardiomyopathy, dilated 1O (CMD1O) [MIM:608569]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:15034580}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Atrial fibrillation, familial, 12 (ATFB12) [MIM:614050]: A familial form of atrial fibrillation, a common sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. {ECO:0000269|PubMed:17245405}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypertrichotic osteochondrodysplasia (HTOCD) [MIM:239850]: A rare disorder characterized by congenital hypertrichosis, neonatal macrosomia, a distinct osteochondrodysplasia, and cardiomegaly. The hypertrichosis leads to thick scalp hair, which extends onto the forehead, and a general increase in body hair. In addition, macrocephaly and coarse facial features, including a broad nasal bridge, epicanthal folds, a wide mouth, and full lips, can be suggestive of a storage disorder. About half of affected individuals are macrosomic and edematous at birth, whereas in childhood they usually have a muscular appearance with little subcutaneous fat. Thickened calvarium, narrow thorax, wide ribs, flattened or ovoid vertebral bodies, coxa valga, osteopenia, enlarged medullary canals, and metaphyseal widening of long bones have been reported. Cardiac manifestations such as patent ductus arteriosus, ventricular hypertrophy, pulmonary hypertension, and pericardial effusions are present in approximately 80% of cases. Motor development is usually delayed due to hypotonia. Most patients have a mild speech delay, and a small percentage have learning difficulties or intellectual disability. {ECO:0000269|PubMed:22608503, ECO:0000269|PubMed:22610116, ECO:0000269|PubMed:26621776}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Subunit of ATP-sensitive potassium channels (KATP). Can form cardiac and smooth muscle-type KATP channels with KCNJ11. KCNJ11 forms the channel pore while ABCC9 is required for activation and regulation. {ECO:0000269|PubMed:9831708}.; ","tcga-gbm",{"$nulls":3},"p.Asn1101Ser","c.3302A>G","MODERATE","1101/1549",26,1,{"$nulls":4},"5","170","273","122","185","148","231","0","0","0","0.1515",{"$nulls":20},"3.273353","-2.32","1.305;.;1.305","0.999979","-2.23;-2.36;-2.23","0.291;.;0.771","0.07;0.037;0.07","0.725;.;0.725",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, dilated, 10; Atrial fibrillation, familial 12; Cantu syndrome","Cardiovascular; Dermatologic; Musculoskeletal",{"$nulls":3},"C0795905| C3279695| C0007193| C1837839","0/0","165,0","0","165","0/1","222,40","0.1527","262",null,"chr12:21844496:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1459"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ABCC9","chr12:21844496","ABCC9(N1101S)",null,null,"topological domain (Cytoplasmic ), domain (ABC transmembrane type-1 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cardiomyopathy, dilated 1O (CMD1O) [MIM:608569]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:15034580}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Atrial fibrillation, familial, 12 (ATFB12) [MIM:614050]: A familial form of atrial fibrillation, a common sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. {ECO:0000269|PubMed:17245405}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypertrichotic osteochondrodysplasia (HTOCD) [MIM:239850]: A rare disorder characterized by congenital hypertrichosis, neonatal macrosomia, a distinct osteochondrodysplasia, and cardiomegaly. The hypertrichosis leads to thick scalp hair, which extends onto the forehead, and a general increase in body hair. In addition, macrocephaly and coarse facial features, including a broad nasal bridge, epicanthal folds, a wide mouth, and full lips, can be suggestive of a storage disorder. About half of affected individuals are macrosomic and edematous at birth, whereas in childhood they usually have a muscular appearance with little subcutaneous fat. Thickened calvarium, narrow thorax, wide ribs, flattened or ovoid vertebral bodies, coxa valga, osteopenia, enlarged medullary canals, and metaphyseal widening of long bones have been reported. Cardiac manifestations such as patent ductus arteriosus, ventricular hypertrophy, pulmonary hypertension, and pericardial effusions are present in approximately 80% of cases. Motor development is usually delayed due to hypotonia. Most patients have a mild speech delay, and a small percentage have learning difficulties or intellectual disability. {ECO:0000269|PubMed:22608503, ECO:0000269|PubMed:22610116, ECO:0000269|PubMed:26621776}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Subunit of ATP-sensitive potassium channels (KATP). Can form cardiac and smooth muscle-type KATP channels with KCNJ11. KCNJ11 forms the channel pore while ABCC9 is required for activation and regulation. {ECO:0000269|PubMed:9831708}.; ","tcga-gbm",{"$nulls":3},"p.Asn1101Ser","c.3302A>G","MODERATE","1101/1549",26,1,{"$nulls":4},"5","170","211","122","145","149","178","0","0","0","0.0618",{"$nulls":20},"3.273353","-2.32","1.305;.;1.305","0.999979","-2.23;-2.36;-2.23","0.291;.;0.771","0.07;0.037;0.07","0.725;.;0.725",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, dilated, 10; Atrial fibrillation, familial 12; Cantu syndrome","Cardiovascular; Dermatologic; Musculoskeletal",{"$nulls":3},"C0795905| C3279695| C0007193| C1837839","0/0","169,0","0","169","0/1","191,14","0.0683","205",null,"chr12:21844496:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0621"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ACAA2","chr18:49787314","ACAA2(L311V)",{"$nulls":3},"helix:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Abolishes BNIP3-mediated apoptosis and mitochondrial damage. {ECO:0000269|PubMed:18371312}.; ","mitocarta",{"$nulls":3},"p.Leu311Val","c.931C>G","MODERATE","311/397",8,{"$nulls":5},"4","159","140","101","93","81","83","0","0","0","0.1566",{"$nulls":20},"2.318094","-2.96","1.32;.;.","0.999915","-2.36;.;.","0.156;.;.","0.198;.;.","0.214;0.212;0.212",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The encoded protein catalyzes the last step of the mitochondrial fatty acid beta-oxidation spiral. Unlike most mitochondrial matrix proteins, it contains a non-cleavable amino-terminal targeting signal. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","117,0","0","117","0/1","99,13","0.1161","112",null,"chr18:49787314:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1398"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ACTN4","chr19:38726956","ACTN4(I732fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Focal segmental glomerulosclerosis 1 (FSGS1) [MIM:603278]: A renal pathology defined by the presence of segmental sclerosis in glomeruli and resulting in proteinuria, reduced glomerular filtration rate and progressive decline in renal function. Renal insufficiency often progresses to end-stage renal disease, a highly morbid state requiring either dialysis therapy or kidney transplantation. {ECO:0000269|PubMed:10700177, ECO:0000269|PubMed:18164029, ECO:0000269|PubMed:18436095, ECO:0000269|PubMed:22351778, ECO:0000269|PubMed:22732337, ECO:0000269|PubMed:23014460, ECO:0000269|PubMed:23890478}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein (Probable). Probably involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation (PubMed:15772161). Involved in tight junction assembly in epithelial cells probably through interaction with MICALL2. Links MICALL2 to the actin cytoskeleton and recruits it to the tight junctions (By similarity). May also function as a transcriptional coactivator, stimulating transcription mediated by the nuclear hormone receptors PPARG and RARA (PubMed:22351778). {ECO:0000250|UniProtKB:P57780, ECO:0000269|PubMed:15772161, ECO:0000269|PubMed:22351778, ECO:0000305|PubMed:9508771}.; ",{"$nulls":4},"p.Ile732fs","c.2193_2194dupCA","HIGH","732/911",18,{"$nulls":5},"3",null,null,"150","149",{"$nulls":11},"(ACTN4|ENSG00000130402|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Focal segmental glomerulosclerosis 1","Renal",{"$nulls":3},"C4551527","0/0","150,0","0","154","0/1","125,15","0.1071","158",null,"chr19:38726956:G:GCA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1074"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ACTR6","chr12:100223865","ACTR6(D381Y)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp381Tyr","c.1141G>T","MODERATE","381/396",11,{"$nulls":5},"5","240","167","162","110","219","155","0","0","0","0.1355",{"$nulls":20},"4.29975","-3.48;-3.48;2.92;2.92","2.22;.;.;.","1","-3.81;-3.88;-3.81;-3.81","0.991;.;0.989;0.991","0.001","0.867;0.86;0.853;0.851",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","236,0","0","236","0/1","139,24","0.1472","163",null,"chr12:100223865:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1273"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ACTR6","chr12:100223865","ACTR6(D381Y)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp381Tyr","c.1141G>T","MODERATE","381/396",11,{"$nulls":5},"5","240","226","162","147","221","202","0","0","0","0.0644",{"$nulls":20},"4.29975","-3.48;-3.48;2.92;2.92","2.22;.;.;.","1","-3.81;-3.88;-3.81;-3.81","0.991;.;0.989;0.991","0.001","0.867;0.86;0.853;0.851",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","236,0","0","236","0/1","207,15","0.0676","222",null,"chr12:100223865:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0544"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ACYP2","chr2:53973805","ACYP2(M19I)",null,null,"domain (Acylphosphatase-like )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Its physiological role is not yet clear.; ","mitocarta",{"$nulls":3},"p.Met19Ile","c.57G>C","MODERATE","19/172",2,{"$nulls":5},"4","208","196","142","124",null,null,"0","0",{"$nulls":22},"0.900704",{"$nulls":6},"0.248;0.231;0.282",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","190,0","0","190","0/1","136,25","0.1553","161",null,"chr2:53973805:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1371"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ADAMTS16","chr5:5306560","ADAMTS16(K1081N)",null,null,"domain (TSP type-1 5 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys1081Asn","c.3243G>T","MODERATE","1081/1224",21,{"$nulls":5},"5","285","370","222","278","236","302","0","0","0","0.1556",{"$nulls":20},"3.041954","0.69","2.685","0.999195","-3.02","0.993","0.011","0.522",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","280,0","0","280","0/1","306,51","0.1429","357",null,"chr5:5306560:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1367"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ADAMTS16","chr5:5306560","ADAMTS16(K1081N)",null,null,"domain (TSP type-1 5 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys1081Asn","c.3243G>T","MODERATE","1081/1224",21,{"$nulls":5},"5","285","348","222","255","235","285","0","0","0","0.0596",{"$nulls":20},"3.041954","0.69","2.685","0.999195","-3.02","0.993","0.011","0.522",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","279,0","0","279","0/1","311,20","0.0604","331",null,"chr5:5306560:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ADAMTSL4","chr1:150557276","ADAMTSL4(S686F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Ectopia lentis 2, isolated, autosomal recessive (ECTOL2) [MIM:225100]: An ocular abnormality characterized by partial or complete displacement of the lens from its space resulting from defective zonule formation. {ECO:0000269|PubMed:19200529}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ectopia lentis et pupillae (ECTOLP) [MIM:225200]: An ocular abnormality characterized by displacement of the lenses and the pupils, associated with other ocular anomalies, but without systemic manifestations. The condition is usually bilateral, with the lenses and pupils displaced in opposite directions. Additional signs include enlarged corneal diameter, increased corneal astigmatism, increased anterior chamber depth, thinning and flattening of the iris with loss of crypts, angle malformation caused by enlarged iris processes, persistent pupillary membrane, loss of zonular fibers, tilted disk, and increased axial length. Secondary manifestations include refractive errors, glaucoma, early cataract development, and retinal detachment. Membrane formation on the posterior aspect of the iris has been observed both in histologic sections and on ultrasound biomicroscopy. {ECO:0000269|PubMed:20702823}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Positive regulation of apoptosis. May facilitate FBN1 microfibril biogenesis. {ECO:0000269|PubMed:16364318, ECO:0000269|PubMed:21989719}.; ",{"$nulls":4},"p.Ser686Phe","c.2057C>T","MODERATE","686/1097",13,{"$nulls":5},"3",null,null,"356","311","318","282",null,null,"0","0.1206",{"$nulls":20},"2.562472","-0.04;0.24;0.04;-0.04","2.945;.;2.945;2.945","0.999986;0.999997;0.999997;0.999997","-2.7;-2.7;-2.61;-2.7","0.944;.;0.967;0.944","0.002;0.003;0.002;0.002","0.341;0.264;0.316;0.342",{"$nulls":3},"Unknown",-1,"AR","Ectopia lentis, isolated, autosomal recessive","Ophthalmologic",{"$nulls":3},"C3541474| C1644196","0/0","422,0","0","450","0/1","340,36","0.0957","407",null,"chr1:150557276:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0932"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ADAMTSL4","chr1:150557276","ADAMTSL4(S686F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Ectopia lentis 2, isolated, autosomal recessive (ECTOL2) [MIM:225100]: An ocular abnormality characterized by partial or complete displacement of the lens from its space resulting from defective zonule formation. {ECO:0000269|PubMed:19200529}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ectopia lentis et pupillae (ECTOLP) [MIM:225200]: An ocular abnormality characterized by displacement of the lenses and the pupils, associated with other ocular anomalies, but without systemic manifestations. The condition is usually bilateral, with the lenses and pupils displaced in opposite directions. Additional signs include enlarged corneal diameter, increased corneal astigmatism, increased anterior chamber depth, thinning and flattening of the iris with loss of crypts, angle malformation caused by enlarged iris processes, persistent pupillary membrane, loss of zonular fibers, tilted disk, and increased axial length. Secondary manifestations include refractive errors, glaucoma, early cataract development, and retinal detachment. Membrane formation on the posterior aspect of the iris has been observed both in histologic sections and on ultrasound biomicroscopy. {ECO:0000269|PubMed:20702823}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Positive regulation of apoptosis. May facilitate FBN1 microfibril biogenesis. {ECO:0000269|PubMed:16364318, ECO:0000269|PubMed:21989719}.; ",{"$nulls":4},"p.Ser686Phe","c.2057C>T","MODERATE","686/1097",13,{"$nulls":5},"4","450","551","356","419","318","369","0","0","0","0.0678",{"$nulls":20},"2.562472","-0.04;0.24;0.04;-0.04","2.945;.;2.945;2.945","0.999986;0.999997;0.999997;0.999997","-2.7;-2.7;-2.61;-2.7","0.944;.;0.967;0.944","0.002;0.003;0.002;0.002","0.341;0.264;0.316;0.342",{"$nulls":3},"Unknown",-1,"AR","Ectopia lentis, isolated, autosomal recessive","Ophthalmologic",{"$nulls":3},"C3541474| C1644196","0/0","418,0","0","418","0/1","454,28","0.0581","482",null,"chr1:150557276:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0549"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ADCY10","chr1:167824740","ADCY10(G1289V)",{"$nulls":6},255,"PASS","Missense","rs1205695359",-1,"DISEASE: Hypercalciuria absorptive 2 (HCA2) [MIM:143870]: A common type of hypercalciuria, a condition characterized by excessive urinary calcium excretion. Absorptive hypercalciuria is due to gastrointestinal hyperabsorption of calcium and is a frequent cause of calcium oxalate nephrolithiasis. {ECO:0000269|PubMed:11932268}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the formation of the signaling molecule cAMP (PubMed:12609998, PubMed:15659711, PubMed:24616449, PubMed:25040695, PubMed:24567411). May function as sensor that mediates responses to changes in cellular bicarbonate and CO(2) levels (PubMed:15659711, PubMed:17591988). Has a critical role in mammalian spermatogenesis by producing the cAMP which regulates cAMP-responsive nuclear factors indispensable for sperm maturation in the epididymis. Induces capacitation, the maturational process that sperm undergo prior to fertilization (By similarity). Involved in ciliary beat regulation (PubMed:17591988). {ECO:0000250|UniProtKB:Q8C0T9, ECO:0000269|PubMed:15659711, ECO:0000269|PubMed:17591988, ECO:0000269|PubMed:24567411, ECO:0000269|PubMed:24616449, ECO:0000269|PubMed:25040695}.; ",{"$nulls":4},"p.Gly1289Val","c.3866G>T","MODERATE","1289/1610",27,{"$nulls":5},"4","650","738","484","525","571","635","0.0015","0.0015","0","0.137",{"$nulls":20},"0.995475","1.54;1.55;1.55",".;2.24;.","0.999902","-1.45",".;0.638;0.753","0.091;0.101;0.09","0.56;0.445;0.391",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0342639","0/0","643,1","0.0016","644","0/1","614,99","0.1388","713",null,"chr1:167824740:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1429"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ADCY10","chr1:167824740","ADCY10(G1289V)",{"$nulls":6},255,"PASS","Missense","rs1205695359",-1,"DISEASE: Hypercalciuria absorptive 2 (HCA2) [MIM:143870]: A common type of hypercalciuria, a condition characterized by excessive urinary calcium excretion. Absorptive hypercalciuria is due to gastrointestinal hyperabsorption of calcium and is a frequent cause of calcium oxalate nephrolithiasis. {ECO:0000269|PubMed:11932268}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the formation of the signaling molecule cAMP (PubMed:12609998, PubMed:15659711, PubMed:24616449, PubMed:25040695, PubMed:24567411). May function as sensor that mediates responses to changes in cellular bicarbonate and CO(2) levels (PubMed:15659711, PubMed:17591988). Has a critical role in mammalian spermatogenesis by producing the cAMP which regulates cAMP-responsive nuclear factors indispensable for sperm maturation in the epididymis. Induces capacitation, the maturational process that sperm undergo prior to fertilization (By similarity). Involved in ciliary beat regulation (PubMed:17591988). {ECO:0000250|UniProtKB:Q8C0T9, ECO:0000269|PubMed:15659711, ECO:0000269|PubMed:17591988, ECO:0000269|PubMed:24567411, ECO:0000269|PubMed:24616449, ECO:0000269|PubMed:25040695}.; ",{"$nulls":4},"p.Gly1289Val","c.3866G>T","MODERATE","1289/1610",27,{"$nulls":5},"4","650","791","484","575","574","696","0.0015","0.0015","0","0.0776",{"$nulls":20},"0.995475","1.54;1.55;1.55",".;2.24;.","0.999902","-1.45",".;0.638;0.753","0.091;0.101;0.09","0.56;0.445;0.391",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0342639","0/0","636,1","0.0016","637","0/1","708,60","0.0781","768",null,"chr1:167824740:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.08"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ADNP","chr20:50902094","ADNP(E42Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential transcription factor. May mediate some of the neuroprotective peptide VIP-associated effects involving normal growth and cancer proliferation.; ","gedi",{"$nulls":3},"p.Glu42Gln","c.124G>C","MODERATE","42/1102",3,{"$nulls":5},"5","141","141","100","102","129","120","0","0","0","0.1167",{"$nulls":20},"2.852326","-0.59;.;.;-0.59;-0.59;-0.59;-0.59","0.69;0.69;.;0.69;0.69;0.69;.","0.963097","-0.87;.;.;-0.87;-0.87;-0.87;-1.0","0.976;0.976;.;0.976;0.976;0.976;.","0.19;.;.;0.19;0.19;0.19;0.095","0.373;0.374;.;0.526;0.373;0.475;.",{"$nulls":3},"Unknown",-1,"AD","Mental retardation, autosomal dominant 28","Cardiovascular; Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C4014538","0/0","140,0","0","140","0/1","122,18","0.1286","140",null,"chr20:50902094:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1176"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ADNP2","chr18:80135655","ADNP2(S81F)",null,null,"zinc finger region (C2H2-type 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ser81Phe","c.242C>T","MODERATE","81/1131",4,{"$nulls":5},"5","310","233","263","199","267","188","0","0","0","0.2234",{"$nulls":20},"3.806226","-0.93","2.8;.;.","0.999975","-4.79;-5.14;-4.84","1.0;.;.","0.0;0.001;0.0","0.889;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","310,0","0","310","0/1","175,53","0.2325","228",null,"chr18:80135655:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2261"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ADNP2","chr18:80135655","ADNP2(S81F)",null,null,"zinc finger region (C2H2-type 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ser81Phe","c.242C>T","MODERATE","81/1131",4,{"$nulls":5},"5","310","300","263","255","266","253","0","0","0","0.0711",{"$nulls":20},"3.806226","-0.93","2.8;.;.","0.999975","-4.79;-5.14;-4.84","1.0;.;.","0.0;0.001;0.0","0.889;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","309,0","0","309","0/1","272,21","0.0717","293",null,"chr18:80135655:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0745"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ADPRHL1","chr13:113403971","ADPRHL1(Insert)",{"$nulls":6},194,"PASS","Large Insertion",{"$nulls":18},"1",{"$nulls":14},"1.1340408E8",{"$nulls":35},"0/0","497,0","0","541","0/1","263,112","0.2154","520",null,"ADPRHL1_gain",0,0,"LargeInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor",null,"0.2154"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","AIM1L","chr1:26345014","AIM1L(V532_V548del)",{"$nulls":6},269,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Val532_Val548del","c.1593_1643delCGTGAAGGGCCCCGGTGCTCCTGATGCCTCATTTCCCACCTGGAAAGAGGT","MODERATE","531/1661",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","271,0","0","272","0/1","216,206","0.6561","314",null,"chr1:26345014:AACCTCTTTCCAGGTGGGAAATGAGGCATCAGGAGCACCGGGGCCCTTCACG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.6561"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ALS2CL","chr3:46672002","ALS2CL(V856L)",{"$nulls":6},255,"PASS","Missense","rs1344842785",-1,null,"FUNCTION: Acts as a guanine nucleotide exchange factor (GEF) for Rab5 GTPase. Regulates the ALS2-mediated endosome dynamics. {ECO:0000269|PubMed:15388334, ECO:0000269|PubMed:16473597, ECO:0000269|PubMed:17239822}.; ",{"$nulls":4},"p.Val856Leu","c.2566G>T","MODERATE","856/953",24,{"$nulls":5},"5","253","238","181","189","201","201","0","0","0","0.1692",{"$nulls":20},"2.671662","1.59","1.7","0.818434;0.730924;0.730924","-2.24","0.099","0.006","0.365",{"$nulls":3},"Unknown",-1,"AD","Schizophrenia","Neurologic",{"$nulls":4},"0/0","242,0","0","242","0/1","186,40","0.177","226",null,"chr3:46672002:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1852"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ALS2CL","chr3:46672002","ALS2CL(V856L)",{"$nulls":6},255,"PASS","Missense","rs1344842785",-1,null,"FUNCTION: Acts as a guanine nucleotide exchange factor (GEF) for Rab5 GTPase. Regulates the ALS2-mediated endosome dynamics. {ECO:0000269|PubMed:15388334, ECO:0000269|PubMed:16473597, ECO:0000269|PubMed:17239822}.; ",{"$nulls":4},"p.Val856Leu","c.2566G>T","MODERATE","856/953",24,{"$nulls":5},"5","253","318","181","252","199","260","0","0","0","0.0577",{"$nulls":20},"2.671662","1.59","1.7","0.818434;0.730924;0.730924","-2.24","0.099","0.006","0.365",{"$nulls":3},"Unknown",-1,"AD","Schizophrenia","Neurologic",{"$nulls":4},"0/0","247,0","0","247","0/1","292,19","0.0611","311",null,"chr3:46672002:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0635"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANAPC13","chr3:134482868","ANAPC13(D13Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. {ECO:0000269|PubMed:15060174, ECO:0000269|PubMed:18485873}.; ","level2",{"$nulls":3},"p.Asp13Tyr","c.37G>T","MODERATE","13/74",2,{"$nulls":5},"4","624","840","416","550","559","741","0","0","0","0.0972",{"$nulls":20},"4.206055",null,null,"1","-8.48","0.956","0.001","0.926;0.937;0.937;0.937",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE",{"$nulls":3},"0/0","595,0","0","595","0/1","709,81","0.1025","790",null,"chr3:134482868:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0909"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ANAPC13","chr3:134482868","ANAPC13(D13Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. The APC/C complex acts by mediating ubiquitination and subsequent degradation of target proteins: it mainly mediates the formation of 'Lys-11'-linked polyubiquitin chains and, to a lower extent, the formation of 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains. {ECO:0000269|PubMed:15060174, ECO:0000269|PubMed:18485873}.; ","level2",{"$nulls":3},"p.Asp13Tyr","c.37G>T","MODERATE","13/74",2,{"$nulls":5},"4","624","876","416","586","559","774","0","0","0","0.0646",{"$nulls":20},"4.206055",null,null,"1","-8.48","0.956","0.001","0.926;0.937;0.937;0.937",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE",{"$nulls":3},"0/0","590,0","0","590","0/1","787,58","0.0686","845",null,"chr3:134482868:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.07"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD11","chr16:89283117","ANKRD11(D1142G)",null,null,"compositionally biased region (Lys-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: KBG syndrome (KBGS) [MIM:148050]: A syndrome characterized by macrodontia of the upper central incisors, distinctive craniofacial findings, short stature, skeletal anomalies, and neurologic involvement that includes global developmental delay, seizures, and intellectual disability. {ECO:0000269|PubMed:21782149, ECO:0000269|PubMed:25413698}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Chromatin regulator which modulates histone acetylation and gene expression in neural precursor cells (By similarity). May recruit histone deacetylases (HDACs) to the p160 coactivators/nuclear receptor complex to inhibit ligand-dependent transactivation (PubMed:15184363). Has a role in proliferation and development of cortical neural precursors (PubMed:25556659). May also regulate bone homeostasis (By similarity). {ECO:0000250|UniProtKB:E9Q4F7, ECO:0000269|PubMed:15184363, ECO:0000269|PubMed:25556659}.; ",{"$nulls":4},"p.Asp1142Gly","c.3425A>G","MODERATE","1142/2663",9,{"$nulls":5},"5","599","538","435","394","481","419","0","0","0","0.4272",{"$nulls":20},"1.497786","0.94;0.94;.","1.59","0.801482","-1.16;-1.16;.","0.0","0.101;0.101;.","0.196;0.159;.",{"$nulls":3},"Unknown",-1,"AD","KBG syndrome","Craniofacial; Dental; Musculoskeletal; Neurologic",{"$nulls":3},"C0220687","0/0","583,0","0","583","0/1","304,217","0.4165","521",null,"chr16:89283117:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3985"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD11","chr16:89283117","ANKRD11(D1142G)",null,null,"compositionally biased region (Lys-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: KBG syndrome (KBGS) [MIM:148050]: A syndrome characterized by macrodontia of the upper central incisors, distinctive craniofacial findings, short stature, skeletal anomalies, and neurologic involvement that includes global developmental delay, seizures, and intellectual disability. {ECO:0000269|PubMed:21782149, ECO:0000269|PubMed:25413698}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Chromatin regulator which modulates histone acetylation and gene expression in neural precursor cells (By similarity). May recruit histone deacetylases (HDACs) to the p160 coactivators/nuclear receptor complex to inhibit ligand-dependent transactivation (PubMed:15184363). Has a role in proliferation and development of cortical neural precursors (PubMed:25556659). May also regulate bone homeostasis (By similarity). {ECO:0000250|UniProtKB:E9Q4F7, ECO:0000269|PubMed:15184363, ECO:0000269|PubMed:25556659}.; ",{"$nulls":4},"p.Asp1142Gly","c.3425A>G","MODERATE","1142/2663",9,{"$nulls":5},"5","599","625","435","477","482","491","0","0","0","0.1935",{"$nulls":20},"1.497786","0.94;0.94;.","1.59","0.801482","-1.16;-1.16;.","0.0","0.101;0.101;.","0.196;0.159;.",{"$nulls":3},"Unknown",-1,"AD","KBG syndrome","Craniofacial; Dental; Musculoskeletal; Neurologic",{"$nulls":3},"C0220687","0/0","580,0","0","580","0/1","497,113","0.1852","610",null,"chr16:89283117:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1824"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD17","chr4:73161256","ANKRD17(E214K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Could play pivotal roles in cell cycle and DNA regulation (PubMed:19150984). Involved in innate immune defense against viruse by positively regulating the viral dsRNA receptors DDX58 and IFIH1 signaling pathways (PubMed:22328336). Involves in NOD2- and NOD1-mediated responses to bacteria suggesting a role in innate antibacterial immune pathways too (PubMed:23711367). Target of enterovirus 71 which is the major etiological agent of HFMD (hand, foot and mouth disease) (PubMed:17276651). Could play a central role for the formation and/or maintenance of the blood vessels of the circulation system (By similarity). {ECO:0000250|UniProtKB:Q99NH0, ECO:0000269|PubMed:17276651, ECO:0000269|PubMed:19150984, ECO:0000269|PubMed:22328336, ECO:0000269|PubMed:23711367}.; ",{"$nulls":4},"p.Glu214Lys","c.640G>A","MODERATE","214/2603",3,{"$nulls":5},"4","370","475","277","336","301","400","0","0","0","0.43",{"$nulls":20},"4.075885","-0.39;-0.36;-0.24;.","2.56;.;2.56;.","0.999994;0.999492;0.996133","-3.22;-3.49;-3.15;.","0.86;.;.;.","0.009;0.01;0.003;.","0.83;0.762;0.754;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","361,0","0","361","0/1","277,184","0.3991","461",null,"chr4:73161256:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.4048"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD17","chr4:73161256","ANKRD17(E214K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Could play pivotal roles in cell cycle and DNA regulation (PubMed:19150984). Involved in innate immune defense against viruse by positively regulating the viral dsRNA receptors DDX58 and IFIH1 signaling pathways (PubMed:22328336). Involves in NOD2- and NOD1-mediated responses to bacteria suggesting a role in innate antibacterial immune pathways too (PubMed:23711367). Target of enterovirus 71 which is the major etiological agent of HFMD (hand, foot and mouth disease) (PubMed:17276651). Could play a central role for the formation and/or maintenance of the blood vessels of the circulation system (By similarity). {ECO:0000250|UniProtKB:Q99NH0, ECO:0000269|PubMed:17276651, ECO:0000269|PubMed:19150984, ECO:0000269|PubMed:22328336, ECO:0000269|PubMed:23711367}.; ",{"$nulls":4},"p.Glu214Lys","c.640G>A","MODERATE","214/2603",3,{"$nulls":5},"4","370","506","277","348","301","414","0","0","0","0.1618",{"$nulls":20},"4.075885","-0.39;-0.36;-0.24;.","2.56;.;2.56;.","0.999994;0.999492;0.996133","-3.22;-3.49;-3.15;.","0.86;.;.;.","0.009;0.01;0.003;.","0.83;0.762;0.754;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","357,0","0","357","0/1","414,78","0.1585","492",null,"chr4:73161256:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1609"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD18A","chr9:38595840","ANKRD18A(K500N)",null,null,"coiled-coil region , splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys500Asn","c.1500G>C","MODERATE","500/992",9,{"$nulls":5},"5","740","891","561","678","676","578","0","0","0","0.2336",{"$nulls":20},"1.997497","2.05","1.7","0.901277","-3.5","0.947","0.107","0.066",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","683,0","0","683","0/1","618,215","0.2581","833",null,"chr9:38595840:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2625"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD18A","chr9:38595840","ANKRD18A(K500N)",null,null,"coiled-coil region , splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys500Asn","c.1500G>C","MODERATE","500/992",9,{"$nulls":5},"4",null,null,"561","635","675","566",null,null,"0","0.0972",{"$nulls":20},"1.997497","2.05","1.7","0.901277","-3.5","0.947","0.107","0.066",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","683,0","0","683","0/1","710,78","0.099","788",null,"chr9:38595840:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1039"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD20A4","chr9:64411250","ANKRD20A4(D655A)",{"$nulls":6},85,"PASS","Missense","rs199885239",3.9959999999999996E-4,{"$nulls":6},"p.Asp655Ala","c.1964A>C","MODERATE","655/823",15,{"$nulls":5},"1",{"$nulls":30},"2.587765","2.24","2.035","0.999966","-5.29","0.997","0.09","0.157",{"$nulls":3},"ExAC_AF",3.9959999999999996E-4,{"$nulls":7},"0/0","70,0","0","70","0/1","65,5","0.0714","70",null,"chr9:64411250:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0714"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANKRD26","chr10:27100098","ANKRD26(D77H)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Thrombocytopenia 2 (THC2) [MIM:188000]: Thrombocytopenia is defined by a decrease in the number of platelets in circulating blood, resulting in the potential for increased bleeding and decreased ability for clotting. {ECO:0000269|PubMed:21211618}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a regulator of adipogenesis. Involved in the regulation of the feeding behavior. {ECO:0000250|UniProtKB:Q811D2}.; ","mitocarta",{"$nulls":3},"p.Asp77His","c.229G>C","MODERATE","77/1726",1,{"$nulls":5},"5","293","351","242","287","215","265","0","0","0","0.1208",{"$nulls":20},"4.177416","0.2",".;3.235","0.638189;0.916515","-4.87;-5.12",".;1.0","0.0","0.529;0.542",{"$nulls":3},"Unknown",-1,"AD","Thrombocytopenia 2","Hematologic",{"$nulls":3},"C1861185","0/0","286,0","0","286","0/1","302,41","0.1195","343",null,"chr10:27100098:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1254"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ANO6","chr12:45416845","ANO6(D741H)",null,null,"transmembrane region (Helical ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Small-conductance calcium-activated nonselective cation (SCAN) channel which acts as a regulator of phospholipid scrambling in platelets and osteoblasts. Phospholipid scrambling results in surface exposure of phosphatidylserine which in platelets is essential to trigger the clotting system whereas in osteoblasts is essential for the deposition of hydroxyapatite during bone mineralization. Has calcium-dependent phospholipid scramblase activity; scrambles phosphatidylserine, phosphatidylcholine and galactosylceramide (By similarity). Can generate outwardly rectifying chloride channel currents in airway epithelial cells and Jurkat T lymphocytes. {ECO:0000250|UniProtKB:Q6P9J9, ECO:0000269|PubMed:20056604, ECO:0000269|PubMed:21107324, ECO:0000269|PubMed:21908539, ECO:0000269|PubMed:22006324, ECO:0000269|PubMed:22946059}.; ",{"$nulls":4},"p.Asp741His","c.2221G>C","MODERATE","741/931",18,{"$nulls":5},"5","270","263","196","178","249","245","0","0","0","0.1878",{"$nulls":20},"3.398256","-0.19","2.715;.;2.715;.","1","-2.89;-2.85;-2.85;-2.73",".;.;0.949;.","0.011;0.016;0.02;0.019","0.323;0.324;0.32;0.318",{"$nulls":3},"Unknown",-1,"AR","Scott syndrome","Hematologic",null,"This gene encodes a multi-pass transmembrane protein that belongs to the anoctamin family. This protein is an essential component for the calcium-dependent exposure of phosphatidylserine on the cell surface. The scrambling of phospholipid occurs in various biological systems, such as when blood platelets are activated, they expose phosphatidylserine to trigger the clotting system. Mutations in this gene are associated with Scott syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011].",null,"C0796149","0/0","268,0","0","268","0/1","209,50","0.1931","259",null,"chr12:45416845:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2022"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ANO6","chr12:45416845","ANO6(D741H)",null,null,"transmembrane region (Helical ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Small-conductance calcium-activated nonselective cation (SCAN) channel which acts as a regulator of phospholipid scrambling in platelets and osteoblasts. Phospholipid scrambling results in surface exposure of phosphatidylserine which in platelets is essential to trigger the clotting system whereas in osteoblasts is essential for the deposition of hydroxyapatite during bone mineralization. Has calcium-dependent phospholipid scramblase activity; scrambles phosphatidylserine, phosphatidylcholine and galactosylceramide (By similarity). Can generate outwardly rectifying chloride channel currents in airway epithelial cells and Jurkat T lymphocytes. {ECO:0000250|UniProtKB:Q6P9J9, ECO:0000269|PubMed:20056604, ECO:0000269|PubMed:21107324, ECO:0000269|PubMed:21908539, ECO:0000269|PubMed:22006324, ECO:0000269|PubMed:22946059}.; ",{"$nulls":4},"p.Asp741His","c.2221G>C","MODERATE","741/931",18,{"$nulls":5},"5","270","269","196","194","249","248","0","0","0","0.0685",{"$nulls":20},"3.398256","-0.19","2.715;.;2.715;.","1","-2.89;-2.85;-2.85;-2.73",".;.;0.949;.","0.011;0.016;0.02;0.019","0.323;0.324;0.32;0.318",{"$nulls":3},"Unknown",-1,"AR","Scott syndrome","Hematologic",null,"This gene encodes a multi-pass transmembrane protein that belongs to the anoctamin family. This protein is an essential component for the calcium-dependent exposure of phosphatidylserine on the cell surface. The scrambling of phospholipid occurs in various biological systems, such as when blood platelets are activated, they expose phosphatidylserine to trigger the clotting system. Mutations in this gene are associated with Scott syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011].",null,"C0796149","0/0","269,0","0","269","0/1","243,21","0.0795","264",null,"chr12:45416845:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0722"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","APOBR","chr16:28497314","APOBR(G758A)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Macrophage receptor that binds to the apolipoprotein B48 (APOB) of dietary triglyceride (TG)-rich lipoproteins (TRL) or to a like domain of APOB in hypertriglyceridemic very low density lipoprotein (HTG-VLDL). Binds and internalizes TRL when out of the context of the macrophage. May provide essential lipids to reticuloendothelial cells. Could also be involved in foam cell formation with elevated TRL and remnant lipoprotein (RLP). Mediates the rapid high-affinity uptake of chylomicrons (CM), HTG- VLDL, and trypsinized (tryp) VLDL devoid of APOE in vitro in macrophages. {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15591219, ECO:0000269|PubMed:9633939}.; ",{"$nulls":4},"p.Gly758Ala","c.2273G>C","MODERATE","758/1097",2,{"$nulls":5},"5","336","280","251","197","295","241","0","0","0","0.2158",{"$nulls":20},"0.520798","-0.29",".;0.345","1","-0.9;-1.17",".;0.126","0.197;0.603","0.051;0.062",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Apolipoprotein B48 receptor is a macrophage receptor that binds to the apolipoprotein B48 of dietary triglyceride (TG)-rich lipoproteins. This receptor may provide essential lipids, lipid-soluble vitamins and other nutrients to reticuloendothelial cells. If overwhelmed with elevated plasma triglyceride, the apolipoprotein B48 receptor may contribute to foam cell formation, endothelial dysfunction, and atherothrombogenesis. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","326,0","0","326","0/1","212,60","0.2206","272",null,"chr16:28497314:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2335"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","APOBR","chr16:28497314","APOBR(G758A)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Macrophage receptor that binds to the apolipoprotein B48 (APOB) of dietary triglyceride (TG)-rich lipoproteins (TRL) or to a like domain of APOB in hypertriglyceridemic very low density lipoprotein (HTG-VLDL). Binds and internalizes TRL when out of the context of the macrophage. May provide essential lipids to reticuloendothelial cells. Could also be involved in foam cell formation with elevated TRL and remnant lipoprotein (RLP). Mediates the rapid high-affinity uptake of chylomicrons (CM), HTG- VLDL, and trypsinized (tryp) VLDL devoid of APOE in vitro in macrophages. {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15591219, ECO:0000269|PubMed:9633939}.; ",{"$nulls":4},"p.Gly758Ala","c.2273G>C","MODERATE","758/1097",2,{"$nulls":5},"5","336","324","251","232","296","278","0","0","0","0.1259",{"$nulls":20},"0.520798","-0.29",".;0.345","1","-0.9;-1.17",".;0.126","0.197;0.603","0.051;0.062",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Apolipoprotein B48 receptor is a macrophage receptor that binds to the apolipoprotein B48 of dietary triglyceride (TG)-rich lipoproteins. This receptor may provide essential lipids, lipid-soluble vitamins and other nutrients to reticuloendothelial cells. If overwhelmed with elevated plasma triglyceride, the apolipoprotein B48 receptor may contribute to foam cell formation, endothelial dysfunction, and atherothrombogenesis. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","326,0","0","326","0/1","280,41","0.1277","321",null,"chr16:28497314:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1379"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","APOBR","chr16:28497872","APOBR(R944T)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Macrophage receptor that binds to the apolipoprotein B48 (APOB) of dietary triglyceride (TG)-rich lipoproteins (TRL) or to a like domain of APOB in hypertriglyceridemic very low density lipoprotein (HTG-VLDL). Binds and internalizes TRL when out of the context of the macrophage. May provide essential lipids to reticuloendothelial cells. Could also be involved in foam cell formation with elevated TRL and remnant lipoprotein (RLP). Mediates the rapid high-affinity uptake of chylomicrons (CM), HTG- VLDL, and trypsinized (tryp) VLDL devoid of APOE in vitro in macrophages. {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15591219, ECO:0000269|PubMed:9633939}.; ",{"$nulls":4},"p.Arg944Thr","c.2831G>C","MODERATE","944/1097",2,{"$nulls":5},"4","291","282","242","209","233","229","0","0","0","0.2751",{"$nulls":20},"0.472055","0.05",".;0.345","1","-0.83;-1.08",".;0.058","0.133;0.12","0.048;0.05",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Apolipoprotein B48 receptor is a macrophage receptor that binds to the apolipoprotein B48 of dietary triglyceride (TG)-rich lipoproteins. This receptor may provide essential lipids, lipid-soluble vitamins and other nutrients to reticuloendothelial cells. If overwhelmed with elevated plasma triglyceride, the apolipoprotein B48 receptor may contribute to foam cell formation, endothelial dysfunction, and atherothrombogenesis. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","289,0","0","289","0/1","204,72","0.2609","276",null,"chr16:28497872:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2679"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","APOBR","chr16:28497872","APOBR(R944T)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Macrophage receptor that binds to the apolipoprotein B48 (APOB) of dietary triglyceride (TG)-rich lipoproteins (TRL) or to a like domain of APOB in hypertriglyceridemic very low density lipoprotein (HTG-VLDL). Binds and internalizes TRL when out of the context of the macrophage. May provide essential lipids to reticuloendothelial cells. Could also be involved in foam cell formation with elevated TRL and remnant lipoprotein (RLP). Mediates the rapid high-affinity uptake of chylomicrons (CM), HTG- VLDL, and trypsinized (tryp) VLDL devoid of APOE in vitro in macrophages. {ECO:0000269|PubMed:10852956, ECO:0000269|PubMed:15591219, ECO:0000269|PubMed:9633939}.; ",{"$nulls":4},"p.Arg944Thr","c.2831G>C","MODERATE","944/1097",2,{"$nulls":5},"4","291","366","242","286","231","291","0","0","0","0.1478",{"$nulls":20},"0.472055","0.05",".;0.345","1","-0.83;-1.08",".;0.058","0.133;0.12","0.048;0.05",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Apolipoprotein B48 receptor is a macrophage receptor that binds to the apolipoprotein B48 of dietary triglyceride (TG)-rich lipoproteins. This receptor may provide essential lipids, lipid-soluble vitamins and other nutrients to reticuloendothelial cells. If overwhelmed with elevated plasma triglyceride, the apolipoprotein B48 receptor may contribute to foam cell formation, endothelial dysfunction, and atherothrombogenesis. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","280,0","0","280","0/1","298,52","0.1486","350",null,"chr16:28497872:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1469"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ARFGAP1","chr20:63284922","ARFGAP1(K268N)",{"$nulls":6},255,"PASS","Missense","rs770390170",1.5490000000000002E-5,null,"FUNCTION: GTPase-activating protein (GAP) for the ADP ribosylation factor 1 (ARF1). Involved in membrane trafficking and /or vesicle transport. Promotes hydrolysis of the ARF1-bound GTP and thus, is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles, a prerequisite for vesicle's fusion with target compartment. Probably regulates ARF1-mediated transport via its interaction with the KDELR proteins and TMED2. Overexpression induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, as when ARF1 is deactivated. Its activity is stimulated by phosphoinosides and inhibited by phosphatidylcholine (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Lys268Asn","c.804G>C","MODERATE","268/414",11,{"$nulls":5},"5","371","561","261","398","326","491","0","0","0","0.0733",{"$nulls":20},"6.6322410000000005","0.36;0.2;1.21;0.37;0.57;1.27;0.28;0.99;1.21",".;.;2.25;.;.;2.25;.;.;.","1","-2.44;-3.15;-2.62;-2.67;-2.7;-2.49;-3.02;-2.5;-2.29",".;.;0.997;.;.;.;.;0.997;.","0.002;0.001;0.001;0.002;0.0;0.032;0.0;0.002;0.0","0.691;0.705;0.652;0.688;.;0.695;.;0.692;.",{"$nulls":3},"ExAC_NFE_AF",1.5490000000000002E-5,{"$nulls":7},"0/0","350,0","0","350","0/1","507,41","0.0748","548",null,"chr20:63284922:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0779"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ARFGAP1","chr20:63284922","ARFGAP1(K268N)",{"$nulls":6},255,"PASS","Missense","rs770390170",1.5490000000000002E-5,null,"FUNCTION: GTPase-activating protein (GAP) for the ADP ribosylation factor 1 (ARF1). Involved in membrane trafficking and /or vesicle transport. Promotes hydrolysis of the ARF1-bound GTP and thus, is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles, a prerequisite for vesicle's fusion with target compartment. Probably regulates ARF1-mediated transport via its interaction with the KDELR proteins and TMED2. Overexpression induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, as when ARF1 is deactivated. Its activity is stimulated by phosphoinosides and inhibited by phosphatidylcholine (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Lys268Asn","c.804G>C","MODERATE","268/414",11,{"$nulls":5},"4","371","527","261","365",null,null,"0","0",{"$nulls":22},"6.6322410000000005","0.36;0.2;1.21;0.37;0.57;1.27;0.28;0.99;1.21",".;.;2.25;.;.;2.25;.;.;.","1","-2.44;-3.15;-2.62;-2.67;-2.7;-2.49;-3.02;-2.5;-2.29",".;.;0.997;.;.;.;.;0.997;.","0.002;0.001;0.001;0.002;0.0;0.032;0.0;0.002;0.0","0.691;0.705;0.652;0.688;.;0.695;.;0.692;.",{"$nulls":3},"ExAC_NFE_AF",1.5490000000000002E-5,{"$nulls":7},"0/0","352,0","0","352","0/1","491,27","0.0521","518",null,"chr20:63284922:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0521"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ARFGEF2","chr20:48973186","ARFGEF2(D523H)",null,null,"region of interest (HUS; DCB:HUS domain interaction )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Periventricular nodular heterotopia 2 (PVNH2) [MIM:608097]: A developmental disorder characterized by the presence of periventricular nodules of cerebral gray matter, resulting from a failure of neurons to migrate normally from the lateral ventricular proliferative zone, where they are formed, to the cerebral cortex. PVNH2 is an autosomal recessive form characterized by microcephaly (small brain), severe developmental delay and recurrent infections. No anomalies extrinsic to the central nervous system, such as dysmorphic features or grossly abnormal endocrine or other conditions, are associated with PVNH2. {ECO:0000269|PubMed:14647276, ECO:0000269|PubMed:23812912, ECO:0000269|PubMed:25160555}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF3 and to a lower extent on ARF5 and ARF6. Promotes the activation of ARF1/ARF5/ARF6 through replacement of GDP with GTP. Involved in the regulation of Golgi vesicular transport. Required for the integrity of the endosomal compartment. Involved in trafficking from the trans-Golgi network (TGN) to endosomes and is required for membrane association of the AP-1 complex and GGA1. Seems to be involved in recycling of the transferrin receptor from recycling endosomes to the plasma membrane. Probably is involved in the exit of GABA(A) receptors from the endoplasmic reticulum. Involved in constitutive release of tumor necrosis factor receptor 1 via exosome-like vesicles; the function seems to involve PKA and specifically PRKAR2B. Proposed to act as A kinase-anchoring protein (AKAP) and may mediate crosstalk between Arf and PKA pathways. {ECO:0000269|PubMed:12051703, ECO:0000269|PubMed:12571360, ECO:0000269|PubMed:15385626, ECO:0000269|PubMed:16477018, ECO:0000269|PubMed:17276987, ECO:0000269|PubMed:18625701, ECO:0000269|PubMed:20360857}.; ",{"$nulls":4},"p.Asp523His","c.1567G>C","MODERATE","523/1785",12,{"$nulls":5},"4","535","573","367","397","474","501","0.0019","0.0019","0","0.0758",{"$nulls":20},"3.222859","0.69","2.965","1","-6.17","0.732","0.016","0.938",{"$nulls":3},"Unknown",-1,"AR","Heterotopia, periventricular, autosomal recessive","Neurologic",{"$nulls":3},"C1842563","0/0","516,1","0.0019","517","0/1","510,42","0.0761","552",null,"chr20:48973186:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0781"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ARHGAP17","chr16:24954727","ARHGAP17(K243T)",null,null,"domain (BAR ), splice variant (In isoform 7. ), splice variant (In isoform 3. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Rho GTPase-activating protein involved in the maintenance of tight junction by regulating the activity of CDC42, thereby playing a central role in apical polarity of epithelial cells. Specifically acts as a GTPase activator for the CDC42 GTPase by converting it to an inactive GDP-bound state. The complex formed with AMOT acts by regulating the uptake of polarity proteins at tight junctions, possibly by deciding whether tight junction transmembrane proteins are recycled back to the plasma membrane or sent elsewhere. Participates in the Ca(2+)-dependent regulation of exocytosis, possibly by catalyzing GTPase activity of Rho family proteins and by inducing the reorganization of the cortical actin filaments. Acts as a GTPase activator in vitro for RAC1. {ECO:0000269|PubMed:11431473, ECO:0000269|PubMed:16678097}.; ",{"$nulls":4},"p.Lys243Thr","c.728A>C","MODERATE","243/881",10,{"$nulls":5},"4","490","605","340","411","466","558","0","0","0","0.0986",{"$nulls":20},"3.137545","1.92;2.03","1.355","0.899462;0.899462;0.996812","-1.2;-1.12","0.985;0.949","0.15;0.09","0.233;0.274",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","451,0","0","451","0/1","510,61","0.1068","571",null,"chr16:24954727:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1046"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ARL6IP4","chr12:122980721","ARL6IP4(L173V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in modulating alternative pre-mRNA splicing with either 5' distal site activation or preferential use of 3' proximal site. In case of infection by Herpes simplex virus (HSVI), may act as a splicing inhibitor of HSVI pre-mRNA. {ECO:0000269|PubMed:19582790}.; ",{"$nulls":4},"p.Leu173Val","c.517C>G","MODERATE","173/421",1,{"$nulls":5},"3",null,null,"39","40",{"$nulls":26},"1.338377",".;.;.;1.14;.","-0.69;-0.69;-0.69;.;-0.69","0.992326;1;1;1;1;0.999546;0.992326;0.992326",".;.;.;-0.03;.",null,".;.;.;0.0;.","0.034;0.072;0.056;.;0.071",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","46,0","0","46","0/1","39,13","0.25","52",null,"chr12:122980721:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.225"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ARL6IP4","chr12:122980721","ARL6IP4(L173V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in modulating alternative pre-mRNA splicing with either 5' distal site activation or preferential use of 3' proximal site. In case of infection by Herpes simplex virus (HSVI), may act as a splicing inhibitor of HSVI pre-mRNA. {ECO:0000269|PubMed:19582790}.; ",{"$nulls":4},"p.Leu173Val","c.517C>G","MODERATE","173/421",1,{"$nulls":5},"5","46","67","39","46","43","61","0","0","0","0.1639",{"$nulls":20},"1.338377",".;.;.;1.14;.","-0.69;-0.69;-0.69;.;-0.69","0.992326;1;1;1;1;0.999546;0.992326;0.992326",".;.;.;-0.03;.",null,".;.;.;0.0;.","0.034;0.072;0.056;.;0.071",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","46,0","0","46","0/1","52,13","0.2","65",null,"chr12:122980721:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2174"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ARMCX4","chrX:101494079","ARMCX4(G1832_A1833insAG)",{"$nulls":6},95,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Gly1832_Ala1833insAlaGly","c.5495_5496insAGCTGG","MODERATE","1832/2290",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","99,0","0","99","0/1","107,6","0.0517","116",null,"chrX:101494079:G:GGCTGGA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0517"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ASPHD1","chr16:29904896","ASPHD1(P332T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro332Thr","c.994C>A","MODERATE","332/390",2,{"$nulls":5},"5","440","426","316","309","358","344","0","0","0","0.0959",{"$nulls":20},"2.436012","1.09",".;.;0.4","0.999999",".;.;1.32",".;.;0.321",".;.;0.462",".;0.769;0.667",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","404,0","0","404","0/1","355,35","0.0897","390",null,"chr16:29904896:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0874"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ASPHD1","chr16:29904896","ASPHD1(P332T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro332Thr","c.994C>A","MODERATE","332/390",2,{"$nulls":5},"5","440","481","316","352","358","386","0","0","0","0.0699",{"$nulls":20},"2.436012","1.09",".;.;0.4","0.999999",".;.;1.32",".;.;0.321",".;.;0.462",".;0.769;0.667",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","404,0","0","404","0/1","424,27","0.0599","451",null,"chr16:29904896:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ASTN1","chr1:177164585","ASTN1(K31T)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Neuronal adhesion molecule that is required for normal migration of young postmitotic neuroblasts along glial fibers, especially in the cerebellum. Required for normal rate of migration of granule cells during brain development and for normal cerebellum development. {ECO:0000250|UniProtKB:Q61137}.; ",{"$nulls":4},"p.Lys31Thr","c.92A>C","MODERATE","31/1294",1,{"$nulls":5},"4","687","887","493","621","624","779","0","0","0","0.1335",{"$nulls":20},"2.028296","2.44;2.86;2.45",".;0;0","0.863769","-0.22;-0.36;-0.23","0.403;0.04;.","0.219;0.236;0.229","0.206;0.296;0.321",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","668,0","0","668","0/1","745,112","0.1307","857",null,"chr1:177164585:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.132"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ATAD2","chr8:123337669","ATAD2(D1003H)",null,null,"domain (Bromo ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.; ",{"$nulls":4},"p.Asp1003His","c.3007G>C","MODERATE","1003/1390",21,1,{"$nulls":4},"5","158","338","118","240","130","301","0","0","0","0.0664",{"$nulls":20},"4.014841","2.36","0.76;.","1","-5.19;-5.41","1.0;.","0.002;0.001","0.639;0.664",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","156,0","0","156","0/1","306,26","0.0783","332",null,"chr8:123337669:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.075"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ATAD2","chr8:123337669","ATAD2(D1003H)",null,null,"domain (Bromo ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.; ",{"$nulls":4},"p.Asp1003His","c.3007G>C","MODERATE","1003/1390",21,1,{"$nulls":4},"5","158","348","118","255","131","296","0","0","0","0.0878",{"$nulls":20},"4.014841","2.36","0.76;.","1","-5.19;-5.41","1.0;.","0.002;0.001","0.639;0.664",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","156,0","0","156","0/1","310,30","0.0882","340",null,"chr8:123337669:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0941"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ATAD5","chr17:30877547","ATAD5(E1306Q)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in DNA damage response. Involved in a RAD9A- related damage checkpoint, a pathway that is important in determining whether DNA damage is compatible with cell survival or whether it requires cell elimination by apoptosis. Modulates the RAD9A interaction with BCL2 and thereby induces DNA damages- induced apoptosis. {ECO:0000269|PubMed:15983387}.; ",{"$nulls":4},"p.Glu1306Gln","c.3916G>C","MODERATE","1306/1844",16,{"$nulls":5},"5","100","66","68","44","95","59","0","0","0","0.1695",{"$nulls":20},"4.630554","1.19","3.26","0.999971","-2.3","1.0","0.001","0.771",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","98,0","0","98","0/1","53,11","0.1719","64",null,"chr17:30877547:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2045"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ATAD5","chr17:30877547","ATAD5(E1306Q)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in DNA damage response. Involved in a RAD9A- related damage checkpoint, a pathway that is important in determining whether DNA damage is compatible with cell survival or whether it requires cell elimination by apoptosis. Modulates the RAD9A interaction with BCL2 and thereby induces DNA damages- induced apoptosis. {ECO:0000269|PubMed:15983387}.; ",{"$nulls":4},"p.Glu1306Gln","c.3916G>C","MODERATE","1306/1844",16,{"$nulls":5},"4","100","103",null,null,"95","96","0","0","0","0.0521",{"$nulls":20},"4.630554","1.19","3.26","0.999971","-2.3","1.0","0.001","0.771",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","99,0","0","99","0/1","95,6","0.0594","101",null,"chr17:30877547:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ATG10","chr5:81987668","ATG10(R33T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E2-like enzyme involved in autophagy. Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5. ATG12 conjugation to ATG5 is required for autophagy. Likely serves as an ATG5-recognition molecule. Not involved in ATG12 conjugation to ATG3 (By similarity). Plays a role in adenovirus-mediated cell lysis. {ECO:0000250, ECO:0000269|PubMed:21367888}.; ",{"$nulls":4},"p.Arg33Thr","c.98G>C","MODERATE","33/220",2,{"$nulls":5},"5","270","208","181","145","222","177","0","0","0","0.1243",{"$nulls":20},"1.719071","1.27;1.9;.;1.9;1.27;0.91","2.24;2.24;.;2.24;2.24;.","0.951724;0.839327;0.839327;0.951724;0.839327","-1.64;-1.51;-5.08;-1.51;-1.64;-1.37","0.974;0.319;.;0.319;0.974;0.089","0.001;0.047;0.006;0.047;0.001;0.059","0.569;0.523;.;0.522;0.569;0.462",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Autophagy is a process for the bulk degradation of cytosolic compartments by lysosomes. ATG10 is an E2-like enzyme involved in 2 ubiquitin-like modifications essential for autophagosome formation: ATG12 (MIM 609608)-ATG5 (MIM 604261) conjugation and modification of a soluble form of MAP-LC3 (MAP1LC3A; MIM 601242), a homolog of yeast Apg8, to a membrane-bound form (Nemoto et al., 2003 [PubMed 12890687]).[supplied by OMIM, Mar 2008].",null,null,"0/0","253,0","0","253","0/1","173,26","0.1307","199",null,"chr5:81987668:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1517"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ATG10","chr5:81987668","ATG10(R33T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E2-like enzyme involved in autophagy. Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5. ATG12 conjugation to ATG5 is required for autophagy. Likely serves as an ATG5-recognition molecule. Not involved in ATG12 conjugation to ATG3 (By similarity). Plays a role in adenovirus-mediated cell lysis. {ECO:0000250, ECO:0000269|PubMed:21367888}.; ",{"$nulls":4},"p.Arg33Thr","c.98G>C","MODERATE","33/220",2,{"$nulls":5},"3",{"$nulls":4},"224","248",null,null,"0","0.0685",{"$nulls":20},"1.719071","1.27;1.9;.;1.9;1.27;0.91","2.24;2.24;.;2.24;2.24;.","0.951724;0.839327;0.839327;0.951724;0.839327","-1.64;-1.51;-5.08;-1.51;-1.64;-1.37","0.974;0.319;.;0.319;0.974;0.089","0.001;0.047;0.006;0.047;0.001;0.059","0.569;0.523;.;0.522;0.569;0.462",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Autophagy is a process for the bulk degradation of cytosolic compartments by lysosomes. ATG10 is an E2-like enzyme involved in 2 ubiquitin-like modifications essential for autophagosome formation: ATG12 (MIM 609608)-ATG5 (MIM 604261) conjugation and modification of a soluble form of MAP-LC3 (MAP1LC3A; MIM 601242), a homolog of yeast Apg8, to a membrane-bound form (Nemoto et al., 2003 [PubMed 12890687]).[supplied by OMIM, Mar 2008].",null,null,"0/0","269,0","0","270","0/1","263,20","0.0707","283",null,"chr5:81987668:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","AXL","chr19:41256499","AXL(K695M)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=AXL and its ligand GAS6 are highly expressed in thyroid carcinoma tissues, and might thus be involved in thyroid tumorigenesis. Overexpression of AXL and its ligand was also detected in many other cancers such as myeloproliferative disorders, prostatic carcinoma cells, or breast cancer.; ","FUNCTION: Receptor tyrosine kinase that transduces signals from the extracellular matrix into the cytoplasm by binding growth factor GAS6 and which is thus regulating many physiological processes including cell survival, cell proliferation, migration and differentiation. Ligand binding at the cell surface induces dimerization and autophosphorylation of AXL. Following activation by ligand, ALX binds and induces tyrosine phosphorylation of PI3- kinase subunits PIK3R1, PIK3R2 and PIK3R3; but also GRB2, PLCG1, LCK and PTPN11. Other downstream substrate candidates for AXL are CBL, NCK2, SOCS1 and TNS2. Recruitment of GRB2 and phosphatidylinositol 3 kinase regulatory subunits by AXL leads to the downstream activation of the AKT kinase. GAS6/AXL signaling plays a role in various processes such as endothelial cell survival during acidification by preventing apoptosis, optimal cytokine signaling during human natural killer cell development, hepatic regeneration, gonadotropin-releasing hormone neuron survival and migration, platelet activation, or regulation of thrombotic responses. Plays also an important role in inhibition of Toll-like receptors (TLRs)-mediated innate immune response. {ECO:0000269|PubMed:10403904, ECO:0000269|PubMed:11484958, ECO:0000269|PubMed:12364394, ECO:0000269|PubMed:12490074, ECO:0000269|PubMed:15507525, ECO:0000269|PubMed:15733062, ECO:0000269|PubMed:1656220, ECO:0000269|PubMed:18840707}.; FUNCTION: (Microbial infection) Acts as a receptor for Ebolavirus, possibly through GAS6 binding to phosphatidyl-serine at the surface of virion envelope. {ECO:0000269|PubMed:22673088}.; ","gedi|foundationOne","[ \"Bosutinib\" , \"Cabozantinib\"]","[ \"Bosutinib\" , \"Cabozantinib\"]","[ \"Bosutinib\" , \"Cabozantinib\"]","p.Lys695Met","c.2084A>T","MODERATE","695/894",18,{"$nulls":5},"4","371","376","274","290","298","300","0","0","0","0.0733",{"$nulls":20},"4.316727","-1.77","2.49;.;.","0.999157","-5.28;-5.28;.","1.0;1.0;.","0.0;0.0;.","0.793;0.81;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0342384","0/0","353,0","0","353","0/1","340,24","0.0659","364",null,"chr19:41256499:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0655"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","BARX2","chr11:129451331","BARX2(E257K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor. Binds optimally to the DNA consensus sequence 5'-YYTAATGRTTTTY-3'. May control the expression of neural adhesion molecules such as L1 or Ng-CAM during embryonic development of both the central and peripherical nervous system. May be involved in controlling adhesive processes in keratinizing epithelia (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu257Lys","c.769G>A","MODERATE","257/279",4,{"$nulls":5},"4","412","414","273","271","371","358","0","0","0","0.1201",{"$nulls":20},"2.490545","-2.59","2.14","0.871766;0.693554;0.693554","-0.61","0.1","0.004","0.315",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","388,0","0","388","0/1","347,47","0.1193","394",null,"chr11:129451331:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.107"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","BCL2L12","chr19:49670264","BCL2L12(D244N)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp244Asn","c.730G>A","MODERATE","244/334",6,{"$nulls":5},"4","369","231","277","179","294","183","0","0","0","0.1639",{"$nulls":20},"1.21158",".;0.89;0.89;.","0;.;0;.","1;1;0.999996",".;-0.03;-0.03;.","0.001;.;0.001;.",".;0.058;0.048;.","0.212;0.182;0.185;0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","357,0","0","357","0/1","185,39","0.1741","224",null,"chr19:49670264:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1564"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","BCL2L12","chr19:49670264","BCL2L12(D244N)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp244Asn","c.730G>A","MODERATE","244/334",6,{"$nulls":5},"4","369","326","277","248","293","253","0","0","0","0.0791",{"$nulls":20},"1.21158",".;0.89;0.89;.","0;.;0;.","1;1;0.999996",".;-0.03;-0.03;.","0.001;.;0.001;.",".;0.058;0.048;.","0.212;0.182;0.185;0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","350,0","0","350","0/1","289,24","0.0767","313",null,"chr19:49670264:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0766"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","BIRC6","chr2:32414931","BIRC6(S547C)",{"$nulls":6},255,"PASS","Missense","rs756116235",1.1580000000000001E-4,null,"FUNCTION: Anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase. Has an unusual ubiquitin conjugation system in that it could combine in a single polypeptide, ubiquitin conjugating (E2) with ubiquitin ligase (E3) activity, forming a chimeric E2/E3 ubiquitin ligase. Its tragets include CASP9 and DIABLO/SMAC. Acts as an inhibitor of CASP3, CASP7 and CASP9. Important regulator for the final stages of cytokinesis. Crucial for normal vesicle targeting to the site of abscission, but also for the integrity of the midbody and the midbody ring, and its striking ubiquitin modification. {ECO:0000269|PubMed:14765125, ECO:0000269|PubMed:15200957, ECO:0000269|PubMed:18329369}.; ",{"$nulls":4},"p.Ser547Cys","c.1640C>G","MODERATE","547/4857",10,{"$nulls":5},"5","253","253","203","199","213","219","0","0","0","0.1096",{"$nulls":20},"1.678833","-0.85",null,"0.978356","-0.68",null,"0.188","0.081",{"$nulls":3},"ExAC_EAS_AF",1.1580000000000001E-4,{"$nulls":7},"0/0","249,0","0","249","0/1","221,28","0.1124","249",null,"chr2:32414931:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1106"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","BIRC6","chr2:32414931","BIRC6(S547C)",{"$nulls":6},255,"PASS","Missense","rs756116235",1.1580000000000001E-4,null,"FUNCTION: Anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase. Has an unusual ubiquitin conjugation system in that it could combine in a single polypeptide, ubiquitin conjugating (E2) with ubiquitin ligase (E3) activity, forming a chimeric E2/E3 ubiquitin ligase. Its tragets include CASP9 and DIABLO/SMAC. Acts as an inhibitor of CASP3, CASP7 and CASP9. Important regulator for the final stages of cytokinesis. Crucial for normal vesicle targeting to the site of abscission, but also for the integrity of the midbody and the midbody ring, and its striking ubiquitin modification. {ECO:0000269|PubMed:14765125, ECO:0000269|PubMed:15200957, ECO:0000269|PubMed:18329369}.; ",{"$nulls":4},"p.Ser547Cys","c.1640C>G","MODERATE","547/4857",10,{"$nulls":5},"5","253","267","203","207","213","220","0","0","0","0.0727",{"$nulls":20},"1.678833","-0.85",null,"0.978356","-0.68",null,"0.188","0.081",{"$nulls":3},"ExAC_EAS_AF",1.1580000000000001E-4,{"$nulls":7},"0/0","249,0","0","249","0/1","239,20","0.0772","259",null,"chr2:32414931:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0628"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","BORA","chr13:72729028","BORA(D105Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for the activation of AURKA at the onset of mitosis. {ECO:0000269|PubMed:16890155}.; ",{"$nulls":4},"p.Asp105Tyr","c.313G>T","MODERATE","105/634",2,{"$nulls":5},"5","259","222","180","160","177","163","0","0","0","0.2883",{"$nulls":20},"4.524637",null,null,"1",null,"1.0;.",null,"0.938;0.948",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","243,0","0","243","0/1","159,57","0.2639","216",null,"chr13:72729028:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2625"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","BORA","chr13:72729028","BORA(D105Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for the activation of AURKA at the onset of mitosis. {ECO:0000269|PubMed:16890155}.; ",{"$nulls":4},"p.Asp105Tyr","c.313G>T","MODERATE","105/634",2,{"$nulls":5},"5","259","210","180","155","182","140","0","0","0","0.0571",{"$nulls":20},"4.524637",null,null,"1",null,"1.0;.",null,"0.938;0.948",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","248,0","0","248","0/1","186,18","0.0882","204",null,"chr13:72729028:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0903"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","BRD4","chr19:15263443","BRD4(V440L)",null,null,"domain (Bromo 2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein. {ECO:0000269|PubMed:11733348, ECO:0000269|PubMed:12543779}.; ","FUNCTION: Chromatin reader protein that recognizes and binds acetylated histones and plays a key role in transmission of epigenetic memory across cell divisions and transcription regulation. Remains associated with acetylated chromatin throughout the entire cell cycle and provides epigenetic memory for postmitotic G1 gene transcription by preserving acetylated chromatin status and maintaining high-order chromatin structure. During interphase, plays a key role in regulating the transcription of signal-inducible genes by associating with the P- TEFb complex and recruiting it to promoters: BRD4 is required to form the transcriptionally active P-TEFb complex by displacing negative regulators such as HEXIM1 and 7SKsnRNA complex from P- TEFb, thereby transforming it into an active form that can then phosphorylate the C-terminal domain (CTD) of RNA polymerase II. Promotes phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II. According to a report, directly acts as an atypical protein kinase and mediates phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II; these data however need additional evidences in vivo (PubMed:22509028). In addition to acetylated histones, also recognizes and binds acetylated RELA, leading to further recruitment of the P-TEFb complex and subsequent activation of NF-kappa-B. Also acts as a regulator of p53/TP53-mediated transcription: following phosphorylation by CK2, recruited to p53/TP53 specific target promoters. {ECO:0000269|PubMed:22509028}.; ","level2",{"$nulls":3},"p.Val440Leu","c.1318G>C","MODERATE","440/1362",7,{"$nulls":5},"5","384","377","272","279","303","310","0","0","0","0.2065",{"$nulls":20},"3.536186","1.48","1.485;1.485;1.485;.","1","-2.9;-2.81;-2.82;.","0.992;0.948;.;.","0.004;0.0;0.002;.","0.694;0.873;0.839;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","370,0","0","370","0/1","287,71","0.1983","358",null,"chr19:15263443:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2007"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","BRD4","chr19:15263443","BRD4(V440L)",null,null,"domain (Bromo 2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein. {ECO:0000269|PubMed:11733348, ECO:0000269|PubMed:12543779}.; ","FUNCTION: Chromatin reader protein that recognizes and binds acetylated histones and plays a key role in transmission of epigenetic memory across cell divisions and transcription regulation. Remains associated with acetylated chromatin throughout the entire cell cycle and provides epigenetic memory for postmitotic G1 gene transcription by preserving acetylated chromatin status and maintaining high-order chromatin structure. During interphase, plays a key role in regulating the transcription of signal-inducible genes by associating with the P- TEFb complex and recruiting it to promoters: BRD4 is required to form the transcriptionally active P-TEFb complex by displacing negative regulators such as HEXIM1 and 7SKsnRNA complex from P- TEFb, thereby transforming it into an active form that can then phosphorylate the C-terminal domain (CTD) of RNA polymerase II. Promotes phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II. According to a report, directly acts as an atypical protein kinase and mediates phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II; these data however need additional evidences in vivo (PubMed:22509028). In addition to acetylated histones, also recognizes and binds acetylated RELA, leading to further recruitment of the P-TEFb complex and subsequent activation of NF-kappa-B. Also acts as a regulator of p53/TP53-mediated transcription: following phosphorylation by CK2, recruited to p53/TP53 specific target promoters. {ECO:0000269|PubMed:22509028}.; ","level2",{"$nulls":3},"p.Val440Leu","c.1318G>C","MODERATE","440/1362",7,{"$nulls":5},"5","384","438","272","330","304","348","0","0","0","0.1437",{"$nulls":20},"3.536186","1.48","1.485;1.485;1.485;.","1","-2.9;-2.81;-2.82;.","0.992;0.948;.;.","0.004;0.0;0.002;.","0.694;0.873;0.839;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","370,0","0","370","0/1","363,56","0.1337","419",null,"chr19:15263443:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1394"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","BSN","chr3:49656595","BSN(A2348fs)",{"$nulls":3},"coiled-coil-region:match_to_sequence_model_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Is thought to be involved in the organization of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. Seems to act through binding to ERC2/CAST1. Essential in regulated neurotransmitter release from a subset of brain glutamatergic synapses. Involved in the formation of the retinal photoreceptor ribbon synapses (By similarity). {ECO:0000250|UniProtKB:O88778}.; ",{"$nulls":4},"p.Ala2348fs","c.7043_7059delCCCTCAGCCGGCCAGGG","HIGH","2348/3926",5,{"$nulls":5},"5","215","164","171","126","168","125","0","0","0","0.104",{"$nulls":5},"(BSN|ENSG00000164061|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","229,0","0","229","0/1","154,19","0.1098","173",null,"chr3:49656595:GGGGCCCTCAGCCGGCCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.127"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","BSN","chr3:49656595","BSN(A2348fs)",{"$nulls":3},"coiled-coil-region:match_to_sequence_model_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Is thought to be involved in the organization of the cytomatrix at the nerve terminals active zone (CAZ) which regulates neurotransmitter release. Seems to act through binding to ERC2/CAST1. Essential in regulated neurotransmitter release from a subset of brain glutamatergic synapses. Involved in the formation of the retinal photoreceptor ribbon synapses (By similarity). {ECO:0000250|UniProtKB:O88778}.; ",{"$nulls":4},"p.Ala2348fs","c.7043_7059delCCCTCAGCCGGCCAGGG","HIGH","2348/3926",5,{"$nulls":5},"4",null,null,"171","148","167","146",null,null,"0","0.0685",{"$nulls":5},"(BSN|ENSG00000164061|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","230,0","0","230","0/1","190,11","0.0547","201",null,"chr3:49656595:GGGGCCCTCAGCCGGCCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0676"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","C14orf178","chr14:77769457","C14orf178(P50A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro50Ala","c.148C>G","MODERATE","50/122",3,{"$nulls":5},"5","119","105","105","99","79","83","0","0","0","0.1687",{"$nulls":20},"0.797661","-1.39","2.075;.","1","-7.66;-7.93","0.903;.","0.009;0.012","0.337;0.338",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","115,0","0","115","0/1","88,17","0.1619","105",null,"chr14:77769457:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1616"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","C14orf178","chr14:77769457","C14orf178(P50A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro50Ala","c.148C>G","MODERATE","50/122",3,{"$nulls":5},"5","119","165","105","145","79","117","0","0","0","0.1538",{"$nulls":20},"0.797661","-1.39","2.075;.","1","-7.66;-7.93","0.903;.","0.009;0.012","0.337;0.338",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","115,0","0","115","0/1","142,22","0.1341","164",null,"chr14:77769457:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1103"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","C19orf68","chr19:48195676","C19orf68(G538R)",{"$nulls":6},255,"PASS","Missense","rs552596343",0.004464,{"$nulls":6},"p.Gly538Arg","c.1612G>C","MODERATE","538/920",4,{"$nulls":5},"5","235","154","191","121","169","115","0","0","0","0.3652",{"$nulls":20},"1.7076280000000001",null,null,"0.999285","-2.89;.","0.18;.","0.011;.","0.147;0.188",{"$nulls":3},"ExAC_SAS_AF",0.004464,{"$nulls":7},"0|0","233,0","0","233","0|1","93,57","0.38","150",null,"chr19:48195676:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3719"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","C19orf68","chr19:48195676","C19orf68(G538R)",{"$nulls":6},255,"PASS","Missense","rs552596343",0.004464,{"$nulls":6},"p.Gly538Arg","c.1612G>C","MODERATE","538/920",4,{"$nulls":5},"5","235","210","191","171","172","160","0","0","0","0.1938",{"$nulls":20},"1.7076280000000001",null,null,"0.999285","-2.89;.","0.18;.","0.011;.","0.147;0.188",{"$nulls":3},"ExAC_SAS_AF",0.004464,{"$nulls":7},"0|0","232,0","0","232","0|1","171,38","0.1818","209",null,"chr19:48195676:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.193"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","C1orf162","chr1:111477407","C1orf162(I61F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ile61Phe","c.181A>T","MODERATE","61/155",4,{"$nulls":5},"4","429","699","314","490","375","591","0","0","0","0.0998",{"$nulls":20},"2.074922","0.52;0.53","1.7","0.846657","-3.69;-3.6","0.385;.","0.0","0.446;0.45",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","403,0","0","403","0/1","606,66","0.0982","672",null,"chr1:111477407:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0878"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","C2orf71","chr2:29070985","C2orf71(M1093V)",{"$nulls":6},255,"PASS","Missense","rs777348261",0.0002333,{"$nulls":6},"p.Met1093Val","c.3277A>G","MODERATE","1093/1288",1,{"$nulls":5},"4","2048","2444","1383","1625","1691","1917","0","0","0","0.1054",{"$nulls":20},"-0.009414","2.41",null,"1","0.92",null,"0.371","0.049",{"$nulls":3},"ExAC_EAS_AF",0.0002333,{"$nulls":7},"0/0","1431,0","0","1431","0/1","1507,194","0.1141","1701",null,"chr2:29070985:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1188"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","C2orf71","chr2:29070985","C2orf71(M1093V)",{"$nulls":6},255,"PASS","Missense","rs777348261",0.0002333,{"$nulls":6},"p.Met1093Val","c.3277A>G","MODERATE","1093/1288",1,{"$nulls":5},"3","2048","2617","1383","1775",null,null,"0","0",{"$nulls":22},"-0.009414","2.41",null,"1","0.92",null,"0.371","0.049",{"$nulls":3},"ExAC_EAS_AF",0.0002333,{"$nulls":7},"0/0","1381,0","0","1381","0/1","1666,96","0.0545","1762",null,"chr2:29070985:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0501"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","C6orf132","chr6:42107284","C6orf132(T210P)",{"$nulls":6},75,"PASS","Missense","rs1161783378",-1,{"$nulls":6},"p.Thr210Pro","c.628A>C","MODERATE","210/1188",4,6,{"$nulls":4},"1",{"$nulls":30},"1.6067900000000002","0.65","2.14","0.910407","-2.49",null,"0.024","0.265",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","124,0","0","124","0/1","84,8","0.087","92",null,"chr6:42107284:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.087"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","C6orf132","chr6:42107344","C6orf132(P184fs)",{"$nulls":6},112,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Pro184fs","c.549_567delGCCCAGCATGGCCCCACCT","HIGH","183/1188",4,{"$nulls":5},"1",{"$nulls":15},"(C6orf132|ENSG00000188112|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","80,0","0","82","0/1","67,12","0.1429","84",null,"chr6:42107344:GAGGTGGGGCCATGCTGGGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1429"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CACNA1F","chrX:49207044","CACNA1F(G1742E)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Night blindness, congenital stationary, 2A (CSNB2A) [MIM:300071]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:11281458, ECO:0000269|PubMed:12111638, ECO:0000269|PubMed:12187427, ECO:0000269|PubMed:15897456, ECO:0000269|PubMed:22194652, ECO:0000269|PubMed:9662399, ECO:0000269|PubMed:9662400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cone-rod dystrophy, X-linked 3 (CORDX3) [MIM:300476]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:16505158}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Aaland island eye disease (AIED) [MIM:300600]: A retinal disease characterized by a combination of fundus hypopigmentation, decreased visual acuity due to foveal hypoplasia, nystagmus, astigmatism, protan color vision defect, myopia, and defective dark adaptation. Except for progression of axial myopia, the disease can be considered to be a stationary condition. Electroretinography reveals abnormalities in both photopic and scotopic functions. {ECO:0000269|PubMed:17525176, ECO:0000269|PubMed:22194652}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 1: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1F gives rise to L-type calcium currents. Long- lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group. They are blocked by dihydropyridines (DHP), phenylalkylamines, and by benzothiazepines. Activates at more negative voltages and does not undergo calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarization. {ECO:0000269|PubMed:27226626}.; FUNCTION: Isoform 6: Voltage-dependent L-type calcium channel activates at more hyperpolarized voltages and exibits a robust calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarizations. {ECO:0000269|PubMed:27226626}.; ","level2",{"$nulls":3},"p.Gly1742Glu","c.5225G>A","MODERATE","1742/1977",44,1,{"$nulls":4},"3",null,null,"481","498","572","590",null,null,"0","0.1356",{"$nulls":20},"0.256509","-3.87;-3.8;-3.79",".;.;1.5","1","-1.53;-1.87;-1.87",".;.;0.011","0.299;0.327;0.312","0.076;0.088;0.09",{"$nulls":3},"Unknown",-1,"XL","Aland Island eye disease; Cone-rod dystrophy, X-linked, 3; Night blindness, congenital stationary, X-linked, type 2A","Ophthalmologic","kMAPK",null,null,"C0268505| C1845407| C1848172","0/0","660,0","0","662","0/1","601,90","0.1302","691",null,"chrX:49207044:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1406"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CACNA1F","chrX:49207044","CACNA1F(G1742E)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Night blindness, congenital stationary, 2A (CSNB2A) [MIM:300071]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:11281458, ECO:0000269|PubMed:12111638, ECO:0000269|PubMed:12187427, ECO:0000269|PubMed:15897456, ECO:0000269|PubMed:22194652, ECO:0000269|PubMed:9662399, ECO:0000269|PubMed:9662400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cone-rod dystrophy, X-linked 3 (CORDX3) [MIM:300476]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:16505158}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Aaland island eye disease (AIED) [MIM:300600]: A retinal disease characterized by a combination of fundus hypopigmentation, decreased visual acuity due to foveal hypoplasia, nystagmus, astigmatism, protan color vision defect, myopia, and defective dark adaptation. Except for progression of axial myopia, the disease can be considered to be a stationary condition. Electroretinography reveals abnormalities in both photopic and scotopic functions. {ECO:0000269|PubMed:17525176, ECO:0000269|PubMed:22194652}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 1: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1F gives rise to L-type calcium currents. Long- lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group. They are blocked by dihydropyridines (DHP), phenylalkylamines, and by benzothiazepines. Activates at more negative voltages and does not undergo calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarization. {ECO:0000269|PubMed:27226626}.; FUNCTION: Isoform 6: Voltage-dependent L-type calcium channel activates at more hyperpolarized voltages and exibits a robust calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarizations. {ECO:0000269|PubMed:27226626}.; ","level2",{"$nulls":3},"p.Gly1742Glu","c.5225G>A","MODERATE","1742/1977",44,1,{"$nulls":4},"4","662","751","481","519","576","649","0","0","0","0.0632",{"$nulls":20},"0.256509","-3.87;-3.8;-3.79",".;.;1.5","1","-1.53;-1.87;-1.87",".;.;0.011","0.299;0.327;0.312","0.076;0.088;0.09",{"$nulls":3},"Unknown",-1,"XL","Aland Island eye disease; Cone-rod dystrophy, X-linked, 3; Night blindness, congenital stationary, X-linked, type 2A","Ophthalmologic","kMAPK",null,null,"C0268505| C1845407| C1848172","0/0","635,0","0","635","0/1","667,49","0.0684","716",null,"chrX:49207044:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0578"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CACNA1I","chr22:39662832","CACNA1I(E1143D)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This channel gives rise to T-type calcium currents. T-type calcium channels belong to the \"low-voltage activated (LVA)\" group and are strongly blocked by nickel and mibefradil. A particularity of this type of channels is an opening at quite negative potentials, and a voltage- dependent inactivation. T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle. They may also be involved in the modulation of firing patterns of neurons which is important for information processing as well as in cell growth processes. Gates in voltage ranges similar to, but higher than alpha 1G or alpha 1H (By similarity). {ECO:0000250}.; ","level2",{"$nulls":3},"p.Glu1143Asp","c.3429G>C","MODERATE","1143/2223",18,{"$nulls":5},"5","614","680","422","461","542","587","0","0","0","0.1056",{"$nulls":20},"2.730447","-4.15;-4.19;-4.18;-4.21",".;2.72;.;2.72","0.969859;0.932352;0.969859;0.932352;0.969859;0.932352","-2.25;-2.26;-2.26;-2.26","0.449;0.801;0.592;0.711","0.202;0.113;0.174;0.084","0.468;0.453;0.455;0.447",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","584,0","0","584","0/1","569,67","0.1053","636",null,"chr22:39662832:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0998"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CADPS","chr3:62518210","CADPS(R778C)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense","rs774579772",1.5040000000000002E-5,null,"FUNCTION: Calcium-binding protein involved in exocytosis of vesicles filled with neurotransmitters and neuropeptides. Probably acts upstream of fusion in the biogenesis or maintenance of mature secretory vesicles. Regulates catecholamine loading of DCVs. May specifically mediate the Ca(2+)-dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles by acting as a PtdIns(4,5)P2-binding protein that acts at prefusion step following ATP-dependent priming and participates in DCVs-membrane fusion. However, it may also participate in small clear synaptic vesicles (SVs) exocytosis and it is unclear whether its function is related to Ca(2+) triggering (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg778Cys","c.2332C>T","MODERATE","778/1353",14,{"$nulls":5},"5","420","403","279","261","389","373","0","0","0","0.1743",{"$nulls":20},"4.457281",".;1.44;1.44;1.44",".;1.87;.;1.87","1",".;-5.53;-5.57;-5.52",".;0.999;0.998;0.995",".;0.0;0.001;0.001","0.765;0.708;0.724;0.73",{"$nulls":3},"ExAC_NFE_AF",1.5040000000000002E-5,{"$nulls":7},"0/0","406,0","0","406","0/1","319,75","0.1904","394",null,"chr3:62518210:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1724"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CADPS","chr3:62518210","CADPS(R778C)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense","rs774579772",1.5040000000000002E-5,null,"FUNCTION: Calcium-binding protein involved in exocytosis of vesicles filled with neurotransmitters and neuropeptides. Probably acts upstream of fusion in the biogenesis or maintenance of mature secretory vesicles. Regulates catecholamine loading of DCVs. May specifically mediate the Ca(2+)-dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles by acting as a PtdIns(4,5)P2-binding protein that acts at prefusion step following ATP-dependent priming and participates in DCVs-membrane fusion. However, it may also participate in small clear synaptic vesicles (SVs) exocytosis and it is unclear whether its function is related to Ca(2+) triggering (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg778Cys","c.2332C>T","MODERATE","778/1353",14,{"$nulls":5},"5","420","436","279","296","389","395","0","0","0","0.1013",{"$nulls":20},"4.457281",".;1.44;1.44;1.44",".;1.87;.;1.87","1",".;-5.53;-5.57;-5.52",".;0.999;0.998;0.995",".;0.0;0.001;0.001","0.765;0.708;0.724;0.73",{"$nulls":3},"ExAC_NFE_AF",1.5040000000000002E-5,{"$nulls":7},"0/0","406,0","0","406","0/1","386,48","0.1106","434",null,"chr3:62518210:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1081"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CAMSAP1","chr9:135821053","CAMSAP1(A1214G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19508979, PubMed:21834987, PubMed:24486153, PubMed:24706919, PubMed:24117850). Specifically recognizes growing microtubule minus-ends and stabilizes microtubules (PubMed:24486153, PubMed:24706919). Acts on free microtubule minus-ends that are not capped by microtubule- nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153, PubMed:24706919). In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (- TIP) that dissociates from microtubules after allowing tubulin incorporation (PubMed:24486153, PubMed:24706919). Through interaction with spectrin may regulate neurite outgrowth (PubMed:24117850). {ECO:0000269|PubMed:19508979, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24117850, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:24706919}.; ",{"$nulls":4},"p.Ala1214Gly","c.3641C>G","MODERATE","1214/1613",12,{"$nulls":5},"5","471","763","374","600","378","619","0","0","0","0.0792",{"$nulls":20},"0.023939","2.5","0.11;.;.","1","-0.89;-0.86;-0.89","0.0;.;0.0","0.515;0.561;0.519","0.069;0.063;0.049",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","446,0","0","446","0/1","670,58","0.0797","728",null,"chr9:135821053:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0767"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CASP1","chr11:105034259","CASP1(Y75H)",null,null,"propeptide , domain (CARD ), splice variant (In isoform Epsilon. ), splice variant (In isoform Gamma and isoform Delta. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Thiol protease that cleaves IL-1 beta between an Asp and an Ala, releasing the mature cytokine which is involved in a variety of inflammatory processes. Important for defense against pathogens. Cleaves and activates sterol regulatory element binding proteins (SREBPs). Can also promote apoptosis. Upon inflammasome activation, during DNA virus infection but not RNA virus challenge, controls antiviral immunity through the cleavage of CGAS, rendering it inactive (PubMed:28314590). {ECO:0000269|PubMed:15498465, ECO:0000269|PubMed:1574116, ECO:0000269|PubMed:28314590, ECO:0000269|PubMed:7876192}.; ",{"$nulls":4},"p.Tyr75His","c.223T>C","MODERATE","75/404",2,{"$nulls":5},"3","469","398","400","336",null,null,"0","0",{"$nulls":22},"-0.576285","2.14;2.14;2.14;2.14;2.14;.",".;0.14;0.14;0.14;.;.","1","-0.45;-0.47;-0.47;-0.27;-0.41;.","0.0;0.0;0.0;0.0;0.001;.","0.511;0.437;0.437;0.475;0.301;.","0.075;0.093;0.096;0.07;0.051;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein which is a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic residues to produce 2 subunits, large and small, that dimerize to form the active enzyme. This gene was identified by its ability to proteolytically cleave and activate the inactive precursor of interleukin-1, a cytokine involved in the processes such as inflammation, septic shock, and wound healing. This gene has been shown to induce cell apoptosis and may function in various developmental stages. Studies of a similar gene in mouse suggest a role in the pathogenesis of Huntington disease. Alternative splicing results in transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2012].",null,null,"0/0","461,0","0","461","0/1","332,56","0.1443","388",null,"chr11:105034259:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1429"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CATSPER1","chr11:66021520","CATSPER1(A556V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spermatogenic failure 7 (SPGF7) [MIM:612997]: An infertility disorder characterized by non-motile sperm or sperm motility below the normal threshold, low sperm count, increased abnormally structured spermatozoa, and reduced semen volume. {ECO:0000269|PubMed:19344877}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Voltage-gated calcium channel that plays a central role in calcium-dependent physiological responses essential for successful fertilization, such as sperm hyperactivation, acrosome reaction and chemotaxis towards the oocyte. {ECO:0000269|PubMed:21412338, ECO:0000269|PubMed:21412339}.; ",{"$nulls":4},"p.Ala556Val","c.1667C>T","MODERATE","556/780",4,{"$nulls":5},"5","240","240","183","185","189","201","0","0","0","0.1841",{"$nulls":20},"3.84891","-4.65","0.975","0.961134","-1.99","0.569","0.238","0.318",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C2751811","0/0","234,0","0","234","0/1","199,39","0.1639","238",null,"chr11:66021520:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1784"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CATSPER1","chr11:66021520","CATSPER1(A556V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spermatogenic failure 7 (SPGF7) [MIM:612997]: An infertility disorder characterized by non-motile sperm or sperm motility below the normal threshold, low sperm count, increased abnormally structured spermatozoa, and reduced semen volume. {ECO:0000269|PubMed:19344877}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Voltage-gated calcium channel that plays a central role in calcium-dependent physiological responses essential for successful fertilization, such as sperm hyperactivation, acrosome reaction and chemotaxis towards the oocyte. {ECO:0000269|PubMed:21412338, ECO:0000269|PubMed:21412339}.; ",{"$nulls":4},"p.Ala556Val","c.1667C>T","MODERATE","556/780",4,{"$nulls":5},"5","240","277","183","215","188","222","0","0","0","0.0766",{"$nulls":20},"3.84891","-4.65","0.975","0.961134","-1.99","0.569","0.238","0.318",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C2751811","0/0","234,0","0","234","0/1","251,23","0.0839","274",null,"chr11:66021520:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0837"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCAR2","chr8:22614460","CCAR2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Core component of the DBIRD complex, a multiprotein complex that acts at the interface between core mRNP particles and RNA polymerase II (RNAPII) and integrates transcript elongation with the regulation of alternative splicing: the DBIRD complex affects local transcript elongation rates and alternative splicing of a large set of exons embedded in (A + T)-rich DNA regions. Inhibits SIRT1 deacetylase activity leading to increasing levels of p53/TP53 acetylation and p53-mediated apoptosis. Inhibits SUV39H1 methyltransferase activity. As part of a histone H3- specific methyltransferase complex may mediate ligand-dependent transcriptional activation by nuclear hormone receptors. Plays a critical role in maintaining genomic stability and cellular integrity following UV-induced genotoxic stress. Regulates the circadian expression of the core clock components NR1D1 and ARNTL/BMAL1. Enhances the transcriptional repressor activity of NR1D1 through stabilization of NR1D1 protein levels by preventing its ubiquitination and subsequent degradation (PubMed:18235501, PubMed:18235502, PubMed:19131338, PubMed:19218236, PubMed:22446626, PubMed:23352644, PubMed:23398316). Represses the ligand-dependent transcriptional activation function of ESR2 (PubMed:20074560). Acts as a regulator of PCK1 expression and gluconeogenesis by a mechanism that involves, at least in part, both NR1D1 and SIRT1 (PubMed:24415752). Negatively regulates the deacetylase activity of HDAC3 and can alter its subcellular localization (PubMed:21030595). Positively regulates the beta- catenin pathway (canonical Wnt signaling pathway) and is required for MCC-mediated repression of the beta-catenin pathway (PubMed:24824780). Represses ligand-dependent transcriptional activation function of NR1H2 and NR1H3 and inhibits the interaction of SIRT1 with NR1H3 (PubMed:25661920). Plays an important role in tumor suppression through p53/TP53 regulation; stabilizes p53/TP53 by affecting its interaction with ubiquitin ligase MDM2 (PubMed:25732823). Represses the transcriptional activator activity of BRCA1 (PubMed:20160719). Inhibits SIRT1 in a CHEK2 and PSEM3-dependent manner and inhibits the activity of CHEK2 in vitro (PubMed:25361978). {ECO:0000269|PubMed:18235501, ECO:0000269|PubMed:18235502, ECO:0000269|PubMed:19131338, ECO:0000269|PubMed:19218236, ECO:0000269|PubMed:20074560, ECO:0000269|PubMed:20160719, ECO:0000269|PubMed:21030595, ECO:0000269|PubMed:22446626, ECO:0000269|PubMed:23352644, ECO:0000269|PubMed:23398316, ECO:0000269|PubMed:24415752, ECO:0000269|PubMed:24824780, ECO:0000269|PubMed:25361978, ECO:0000269|PubMed:25661920, ECO:0000269|PubMed:25732823}.; ",{"$nulls":4},"p.Glu334_Lys347del","c.1000_1041+31delGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCATT","HIGH","334/923",10,{"$nulls":20},"22614533",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr8:22614460:CTGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCAT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf","structuralVariantFile","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CCAR2","chr8:22614460","CCAR2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Core component of the DBIRD complex, a multiprotein complex that acts at the interface between core mRNP particles and RNA polymerase II (RNAPII) and integrates transcript elongation with the regulation of alternative splicing: the DBIRD complex affects local transcript elongation rates and alternative splicing of a large set of exons embedded in (A + T)-rich DNA regions. Inhibits SIRT1 deacetylase activity leading to increasing levels of p53/TP53 acetylation and p53-mediated apoptosis. Inhibits SUV39H1 methyltransferase activity. As part of a histone H3- specific methyltransferase complex may mediate ligand-dependent transcriptional activation by nuclear hormone receptors. Plays a critical role in maintaining genomic stability and cellular integrity following UV-induced genotoxic stress. Regulates the circadian expression of the core clock components NR1D1 and ARNTL/BMAL1. Enhances the transcriptional repressor activity of NR1D1 through stabilization of NR1D1 protein levels by preventing its ubiquitination and subsequent degradation (PubMed:18235501, PubMed:18235502, PubMed:19131338, PubMed:19218236, PubMed:22446626, PubMed:23352644, PubMed:23398316). Represses the ligand-dependent transcriptional activation function of ESR2 (PubMed:20074560). Acts as a regulator of PCK1 expression and gluconeogenesis by a mechanism that involves, at least in part, both NR1D1 and SIRT1 (PubMed:24415752). Negatively regulates the deacetylase activity of HDAC3 and can alter its subcellular localization (PubMed:21030595). Positively regulates the beta- catenin pathway (canonical Wnt signaling pathway) and is required for MCC-mediated repression of the beta-catenin pathway (PubMed:24824780). Represses ligand-dependent transcriptional activation function of NR1H2 and NR1H3 and inhibits the interaction of SIRT1 with NR1H3 (PubMed:25661920). Plays an important role in tumor suppression through p53/TP53 regulation; stabilizes p53/TP53 by affecting its interaction with ubiquitin ligase MDM2 (PubMed:25732823). Represses the transcriptional activator activity of BRCA1 (PubMed:20160719). Inhibits SIRT1 in a CHEK2 and PSEM3-dependent manner and inhibits the activity of CHEK2 in vitro (PubMed:25361978). {ECO:0000269|PubMed:18235501, ECO:0000269|PubMed:18235502, ECO:0000269|PubMed:19131338, ECO:0000269|PubMed:19218236, ECO:0000269|PubMed:20074560, ECO:0000269|PubMed:20160719, ECO:0000269|PubMed:21030595, ECO:0000269|PubMed:22446626, ECO:0000269|PubMed:23352644, ECO:0000269|PubMed:23398316, ECO:0000269|PubMed:24415752, ECO:0000269|PubMed:24824780, ECO:0000269|PubMed:25361978, ECO:0000269|PubMed:25661920, ECO:0000269|PubMed:25732823}.; ",{"$nulls":4},"p.Glu334_Lys347del","c.1000_1041+31delGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCATT","HIGH","334/923",10,{"$nulls":20},"22614533",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr8:22614460:CTGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCAT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf","structuralVariantFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCAR2","chr8:22614460","CCAR2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Core component of the DBIRD complex, a multiprotein complex that acts at the interface between core mRNP particles and RNA polymerase II (RNAPII) and integrates transcript elongation with the regulation of alternative splicing: the DBIRD complex affects local transcript elongation rates and alternative splicing of a large set of exons embedded in (A + T)-rich DNA regions. Inhibits SIRT1 deacetylase activity leading to increasing levels of p53/TP53 acetylation and p53-mediated apoptosis. Inhibits SUV39H1 methyltransferase activity. As part of a histone H3- specific methyltransferase complex may mediate ligand-dependent transcriptional activation by nuclear hormone receptors. Plays a critical role in maintaining genomic stability and cellular integrity following UV-induced genotoxic stress. Regulates the circadian expression of the core clock components NR1D1 and ARNTL/BMAL1. Enhances the transcriptional repressor activity of NR1D1 through stabilization of NR1D1 protein levels by preventing its ubiquitination and subsequent degradation (PubMed:18235501, PubMed:18235502, PubMed:19131338, PubMed:19218236, PubMed:22446626, PubMed:23352644, PubMed:23398316). Represses the ligand-dependent transcriptional activation function of ESR2 (PubMed:20074560). Acts as a regulator of PCK1 expression and gluconeogenesis by a mechanism that involves, at least in part, both NR1D1 and SIRT1 (PubMed:24415752). Negatively regulates the deacetylase activity of HDAC3 and can alter its subcellular localization (PubMed:21030595). Positively regulates the beta- catenin pathway (canonical Wnt signaling pathway) and is required for MCC-mediated repression of the beta-catenin pathway (PubMed:24824780). Represses ligand-dependent transcriptional activation function of NR1H2 and NR1H3 and inhibits the interaction of SIRT1 with NR1H3 (PubMed:25661920). Plays an important role in tumor suppression through p53/TP53 regulation; stabilizes p53/TP53 by affecting its interaction with ubiquitin ligase MDM2 (PubMed:25732823). Represses the transcriptional activator activity of BRCA1 (PubMed:20160719). Inhibits SIRT1 in a CHEK2 and PSEM3-dependent manner and inhibits the activity of CHEK2 in vitro (PubMed:25361978). {ECO:0000269|PubMed:18235501, ECO:0000269|PubMed:18235502, ECO:0000269|PubMed:19131338, ECO:0000269|PubMed:19218236, ECO:0000269|PubMed:20074560, ECO:0000269|PubMed:20160719, ECO:0000269|PubMed:21030595, ECO:0000269|PubMed:22446626, ECO:0000269|PubMed:23352644, ECO:0000269|PubMed:23398316, ECO:0000269|PubMed:24415752, ECO:0000269|PubMed:24824780, ECO:0000269|PubMed:25361978, ECO:0000269|PubMed:25661920, ECO:0000269|PubMed:25732823}.; ",{"$nulls":4},"p.Glu334_Lys347del","c.1000_1041+31delGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCATT","HIGH","334/923",10,{"$nulls":5},"4",null,null,"250","160","109","117",null,null,"0","0.3761",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","398,2","0.005","400","0/1","220,52","0.1912","272",null,"chr8:22614460:CTGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCAT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.175"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CCAR2","chr8:22614460","CCAR2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Core component of the DBIRD complex, a multiprotein complex that acts at the interface between core mRNP particles and RNA polymerase II (RNAPII) and integrates transcript elongation with the regulation of alternative splicing: the DBIRD complex affects local transcript elongation rates and alternative splicing of a large set of exons embedded in (A + T)-rich DNA regions. Inhibits SIRT1 deacetylase activity leading to increasing levels of p53/TP53 acetylation and p53-mediated apoptosis. Inhibits SUV39H1 methyltransferase activity. As part of a histone H3- specific methyltransferase complex may mediate ligand-dependent transcriptional activation by nuclear hormone receptors. Plays a critical role in maintaining genomic stability and cellular integrity following UV-induced genotoxic stress. Regulates the circadian expression of the core clock components NR1D1 and ARNTL/BMAL1. Enhances the transcriptional repressor activity of NR1D1 through stabilization of NR1D1 protein levels by preventing its ubiquitination and subsequent degradation (PubMed:18235501, PubMed:18235502, PubMed:19131338, PubMed:19218236, PubMed:22446626, PubMed:23352644, PubMed:23398316). Represses the ligand-dependent transcriptional activation function of ESR2 (PubMed:20074560). Acts as a regulator of PCK1 expression and gluconeogenesis by a mechanism that involves, at least in part, both NR1D1 and SIRT1 (PubMed:24415752). Negatively regulates the deacetylase activity of HDAC3 and can alter its subcellular localization (PubMed:21030595). Positively regulates the beta- catenin pathway (canonical Wnt signaling pathway) and is required for MCC-mediated repression of the beta-catenin pathway (PubMed:24824780). Represses ligand-dependent transcriptional activation function of NR1H2 and NR1H3 and inhibits the interaction of SIRT1 with NR1H3 (PubMed:25661920). Plays an important role in tumor suppression through p53/TP53 regulation; stabilizes p53/TP53 by affecting its interaction with ubiquitin ligase MDM2 (PubMed:25732823). Represses the transcriptional activator activity of BRCA1 (PubMed:20160719). Inhibits SIRT1 in a CHEK2 and PSEM3-dependent manner and inhibits the activity of CHEK2 in vitro (PubMed:25361978). {ECO:0000269|PubMed:18235501, ECO:0000269|PubMed:18235502, ECO:0000269|PubMed:19131338, ECO:0000269|PubMed:19218236, ECO:0000269|PubMed:20074560, ECO:0000269|PubMed:20160719, ECO:0000269|PubMed:21030595, ECO:0000269|PubMed:22446626, ECO:0000269|PubMed:23352644, ECO:0000269|PubMed:23398316, ECO:0000269|PubMed:24415752, ECO:0000269|PubMed:24824780, ECO:0000269|PubMed:25361978, ECO:0000269|PubMed:25661920, ECO:0000269|PubMed:25732823}.; ",{"$nulls":4},"p.Glu334_Lys347del","c.1000_1041+31delGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCATT","HIGH","334/923",10,{"$nulls":5},"4",null,null,"250","248","109","146",null,null,"0","0.1781",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","399,2","0.005","401","0/1","373,31","0.0767","404",null,"chr8:22614460:CTGAGCCAAGGGAGACGCCAGAGCATCCTCTGAAGCAGATTAAGGTAAGAGCTGGAGAGCAGGAGGAGATGCAT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0766"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCDC40","chr17:80084794","CCDC40(I681fs)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 4. )","coiled-coil-region:match_to_sequence_model_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,"DISEASE: Ciliary dyskinesia, primary, 15 (CILD15) [MIM:613808]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:21131974, ECO:0000269|PubMed:22693285, ECO:0000269|PubMed:23255504, ECO:0000269|PubMed:23402890, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease is characterized by primary ciliary dyskinesia with inner dynein arm (IDA) defects and axonemal dizorganisation: defects in CCDC39 and CCDC40 constitute the major cause of this phenotype. {ECO:0000269|PubMed:22693285, ECO:0000269|PubMed:23255504}.; ","FUNCTION: Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131974). Probably acts together with CCDC39 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly. Required for axonemal recruitment of CCDC39 (PubMed:21131974). {ECO:0000250|UniProtKB:A8IQT2, ECO:0000269|PubMed:21131974}.; ",{"$nulls":4},"p.Ile681fs","c.2042_2060delTCACACACACCAGCAGCAG","HIGH","681/1142",13,{"$nulls":5},"5","361","232","292","187","338","229","0","0","0","0.2358",{"$nulls":5},"(CCDC40|ENSG00000141519|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Ciliary dyskinesia, primary, 15","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary",{"$nulls":3},"C3151137","0/0","428,0","0","428","0/1","194,59","0.2332","253",null,"chr17:80084794:ATCACACACACCAGCAGCAG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2781"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CCDC40","chr17:80084794","CCDC40(I681fs)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 4. )","coiled-coil-region:match_to_sequence_model_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,"DISEASE: Ciliary dyskinesia, primary, 15 (CILD15) [MIM:613808]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:21131974, ECO:0000269|PubMed:22693285, ECO:0000269|PubMed:23255504, ECO:0000269|PubMed:23402890, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease is characterized by primary ciliary dyskinesia with inner dynein arm (IDA) defects and axonemal dizorganisation: defects in CCDC39 and CCDC40 constitute the major cause of this phenotype. {ECO:0000269|PubMed:22693285, ECO:0000269|PubMed:23255504}.; ","FUNCTION: Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131974). Probably acts together with CCDC39 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly. Required for axonemal recruitment of CCDC39 (PubMed:21131974). {ECO:0000250|UniProtKB:A8IQT2, ECO:0000269|PubMed:21131974}.; ",{"$nulls":4},"p.Ile681fs","c.2042_2060delTCACACACACCAGCAGCAG","HIGH","681/1142",13,{"$nulls":5},"5","361","325","292","262","337","315","0","0","0","0.1206",{"$nulls":5},"(CCDC40|ENSG00000141519|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Ciliary dyskinesia, primary, 15","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary",{"$nulls":3},"C3151137","0/0","428,0","0","428","0/1","347,38","0.0987","385",null,"chr17:80084794:ATCACACACACCAGCAGCAG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1336"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCDC7","chr10:32456315","CCDC7(A146G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumorigenesis. {ECO:0000250|UniProtKB:Q9D541}.; ",{"$nulls":4},"p.Ala146Gly","c.437C>G","MODERATE","146/486",4,{"$nulls":5},"5","243","291","153","183","228","267","0","0","0","0.0712",{"$nulls":20},"2.868052","0.08;0.08;0.08;0.08;0.08;.","2.255;2.255;.;.;.;2.255","0.705514","-2.42;-2.42;-3.45;-3.45;-3.45;.",".;.;0.997;.;.;0.997","0.0;0.0;0.0;0.0;0.0;.","0.539;0.539;0.555;0.554;0.556;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","238,0","0","238","0/1","261,25","0.0874","286",null,"chr10:32456315:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0765"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CCDC7","chr10:32456315","CCDC7(A146G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumorigenesis. {ECO:0000250|UniProtKB:Q9D541}.; ",{"$nulls":4},"p.Ala146Gly","c.437C>G","MODERATE","146/486",4,{"$nulls":5},"5","243","294","153","185","228","267","0","0","0","0.0824",{"$nulls":20},"2.868052","0.08;0.08;0.08;0.08;0.08;.","2.255;2.255;.;.;.;2.255","0.705514","-2.42;-2.42;-3.45;-3.45;-3.45;.",".;.;0.997;.;.;0.997","0.0;0.0;0.0;0.0;0.0;.","0.539;0.539;0.555;0.554;0.556;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","238,0","0","238","0/1","263,26","0.09","289",null,"chr10:32456315:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0757"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCDC83","chr11:85919361","CCDC83(L396V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu396Val","c.1186T>G","MODERATE","396/444",12,1,{"$nulls":4},"4","131","150",null,null,"101","112","0","0","0","0.1339",{"$nulls":20},"1.965503","0.94",".;2.685","0.998174","-1.86;-2.15","0.995;0.99","0.006","0.414;0.4",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","118,0","0","118","0/1","117,18","0.1333","135",null,"chr11:85919361:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CCDC83","chr11:85919361","CCDC83(L396V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu396Val","c.1186T>G","MODERATE","396/444",12,1,{"$nulls":4},"5","131","171","103","125","102","143","0","0","0","0.0629",{"$nulls":20},"1.965503","0.94",".;2.685","0.998174","-1.86;-2.15","0.995;0.99","0.006","0.414;0.4",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","125,0","0","125","0/1","157,10","0.0599","167",null,"chr11:85919361:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.056"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCDC88C","chr14:91313979","CCDC88C(F611_E612del)",null,null,"coiled-coil region , splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,"DISEASE: Hydrocephalus, congenital, 1 (HYC1) [MIM:236600]: A form of congenital hydrocephalus, a disease characterized by onset in utero of enlarged ventricles due to accumulation of ventricular cerebrospinal fluid. Affected individuals may have neurologic impairment. HYC1 inheritance is autosomal recessive. {ECO:0000269|PubMed:21031079, ECO:0000269|PubMed:23042809}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinocerebellar ataxia 40 (SCA40) [MIM:616053]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA40 is an autosomal dominant, slowly progressive form. Brain MRI shows pontocerebellar atrophy along with a global reduction in brain volume. {ECO:0000269|PubMed:25062847}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Negative regulator of the canonical Wnt signaling pathway, acting downstream of DVL to inhibit CTNNB1/Beta-catenin stabilization (By similarity). May also activate the JNK signaling pathway (PubMed:25062847). {ECO:0000250|UniProtKB:Q6VGS5, ECO:0000269|PubMed:25062847}.; ",{"$nulls":4},"p.Phe611_Glu612del","c.1831_1836delTTTGAG","MODERATE","611/2028",15,{"$nulls":5},"5","329","325","256","254","284","281","0","0","0","0.1068",{"$nulls":31},"Unknown",-1,"AD","Spinocerebellar ataxia 40","Neurologic",{"$nulls":3},"C4518336| C3887608","0/0","309,0","0","309","0/1","267,37","0.1217","304",null,"chr14:91313979:TCTCAAA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1181"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCNE1","chr19:29820838","CCNE1(A200G)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Essential for the control of the cell cycle at the G1/S (start) transition. {ECO:0000269|PubMed:7739542}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Ala200Gly","c.599C>G","MODERATE","200/410",7,{"$nulls":5},"3",null,null,"69","58",{"$nulls":26},"3.390126","2.41;2.41;2.41;.;2.41","3.36;.;.;.;.","1","-2.98;.;-2.98;.;.","0.681;.;.;.;.","0.01;.;0.007;.;.","0.678;.;0.676;0.666;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kCELL_CYCLE,kP53",{"$nulls":3},"0/0","105,0","0","106","0/1","80,6","0.0698","86",null,"chr19:29820838:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.069"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CCT2","chr12:69589629","CCT2(E197D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.; ",{"$nulls":4},"p.Glu197Asp","c.591G>C","MODERATE","197/535",7,{"$nulls":5},"5","186","227","119","151","169","207","0","0","0","0.1111",{"$nulls":20},"1.360011","-1.14","-1.035;.;.","0.99894","0.31;0.31;0.55","0.0;0.0;.","1.0","0.357;0.349;0.36",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","184,0","0","184","0/1","194,28","0.1261","222",null,"chr12:69589629:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1126"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CCT2","chr12:69589629","CCT2(E197D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.; ",{"$nulls":4},"p.Glu197Asp","c.591G>C","MODERATE","197/535",7,{"$nulls":5},"5","186","233","119","154","172","221","0","0","0","0.0588",{"$nulls":20},"1.360011","-1.14","-1.035;.;.","0.99894","0.31;0.31;0.55","0.0;0.0;.","1.0","0.357;0.349;0.36",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","178,0","0","178","0/1","217,14","0.0606","231",null,"chr12:69589629:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0649"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CD1D","chr1:158182995","CD1D(E242V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:17475845}.; ","gedi",{"$nulls":3},"p.Glu242Val","c.725A>T","MODERATE","242/335",5,{"$nulls":5},"4","902","1193","683","916","739","1004","0","0","0","0.2321",{"$nulls":20},"3.936175","4.07","3.125","0.985157","-6.25","0.979","0.001","0.264",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","857,0","0","857","0/1","873,272","0.2376","1145",null,"chr1:158182995:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2336"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CD1D","chr1:158182995","CD1D(E242V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. {ECO:0000269|PubMed:17475845}.; ","gedi",{"$nulls":3},"p.Glu242Val","c.725A>T","MODERATE","242/335",5,{"$nulls":5},"4","902","1116","683","835","741","947","0","0","0","0.1478",{"$nulls":20},"3.936175","4.07","3.125","0.985157","-6.25","0.979","0.001","0.264",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","858,0","0","858","0/1","929,150","0.139","1079",null,"chr1:158182995:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1353"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CDC42BPA","chr1:227080966","CDC42BPA(E803K)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine-protein kinase which is an important downstream effector of CDC42 and plays a role in the regulation of cytoskeleton reorganization and cell migration (PubMed:15723050, PubMed:9418861, PubMed:9092543). Regulates actin cytoskeletal reorganization via phosphorylation of PPP1R12C and MYL9/MLC2 (PubMed:21457715). In concert with MYO18A and LURAP1, is involved in modulating lamellar actomyosin retrograde flow that is crucial to cell protrusion and migration (PubMed:18854160). Phosphorylates: PPP1R12A, LIMK1 and LIMK2 (PubMed:11340065, PubMed:11399775). May play a role in TFRC-mediated iron uptake (PubMed:20188707). In concert with FAM89B/LRAP25 mediates the targeting of LIMK1 to the lamellipodium resulting in its activation and subsequent phosphorylation of CFL1 which is important for lamellipodial F-actin regulation (By similarity). {ECO:0000250|UniProtKB:Q3UU96, ECO:0000269|PubMed:11340065, ECO:0000269|PubMed:11399775, ECO:0000269|PubMed:15723050, ECO:0000269|PubMed:18854160, ECO:0000269|PubMed:20188707, ECO:0000269|PubMed:21457715, ECO:0000269|PubMed:9092543, ECO:0000269|PubMed:9418861}.; ",{"$nulls":4},"p.Glu803Lys","c.2407G>A","MODERATE","803/1732",17,{"$nulls":5},"5","510","611","318","392","476","566","0","0","0","0.1237",{"$nulls":20},"3.023263","0.87;0.87;0.87;.;0.87",".;1.895;1.895;.;.","0.999998;1;0.999998;0.999998;0.999998;1;0.999998","-2.16;-2.29;-2.54;.;-2.41","0.032;.;0.124;.;.","0.031;0.04;0.04;.;0.093","0.488;0.489;0.505;0.375;0.53",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","494,0","0","494","0/1","519,79","0.1321","598",null,"chr1:227080966:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1378"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CDK18","chr1:205527876","CDK18(L301P)",null,null,"domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in signal transduction cascades in terminally differentiated cells.; ",{"$nulls":4},"p.Leu301Pro","c.902T>C","MODERATE","301/504",9,{"$nulls":5},"5","353","311","270","239","303","253","0","0","0","0.2292",{"$nulls":20},"4.579665","0.5",null,"1","-6.65;-6.64;-6.65",".;1.0;.","0.0","0.997;0.997;0.996",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","336,0","0","336","0/1","239,65","0.2138","304",null,"chr1:205527876:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2301"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CDK18","chr1:205527876","CDK18(L301P)",null,null,"domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in signal transduction cascades in terminally differentiated cells.; ",{"$nulls":4},"p.Leu301Pro","c.902T>C","MODERATE","301/504",9,{"$nulls":5},"5","353","357","270","278","302","296","0","0","0","0.1453",{"$nulls":20},"4.579665","0.5",null,"1","-6.65;-6.64;-6.65",".;1.0;.","0.0","0.997;0.997;0.996",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","336,0","0","336","0/1","301,51","0.1449","352",null,"chr1:205527876:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1475"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CENPF","chr1:214630637","CENPF(N433S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Stromme syndrome (STROMS) [MIM:243605]: An autosomal recessive congenital disorder characterized by intestinal atresia, ocular anomalies, microcephaly, and renal and cardiac abnormalities in some patients. The disease has features of a ciliopathy, and lethality in early childhood is observed in severe cases. {ECO:0000269|PubMed:25564561, ECO:0000269|PubMed:26820108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for kinetochore function and chromosome segregation in mitosis. Required for kinetochore localization of dynein, LIS1, NDE1 and NDEL1. Regulates recycling of the plasma membrane by acting as a link between recycling vesicles and the microtubule network though its association with STX4 and SNAP25. Acts as a potential inhibitor of pocket protein-mediated cellular processes during development by regulating the activity of RB proteins during cell division and proliferation. May play a regulatory or permissive role in the normal embryonic cardiomyocyte cell cycle and in promoting continued mitosis in transformed, abnormally dividing neonatal cardiomyocytes. Interaction with RB directs embryonic stem cells toward a cardiac lineage. Involved in the regulation of DNA synthesis and hence cell cycle progression, via its C-terminus. Has a potential role regulating skeletal myogenesis and in cell differentiation in embryogenesis. Involved in dendritic cell regulation of T-cell immunity against chlamydia. {ECO:0000269|PubMed:12974617, ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:7542657, ECO:0000269|PubMed:7651420}.; ",{"$nulls":4},"p.Asn433Ser","c.1298A>G","MODERATE","433/3114",9,{"$nulls":5},"3","204","246",{"$nulls":4},"0","0",{"$nulls":22},"0.897834","-1.11",null,"1","-2.73","0.852","0.08","0.171",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein that associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. In late G2 the protein associates with the kinetochore and maintains this association through early anaphase. It localizes to the spindle midzone and the intracellular bridge in late anaphase and telophase, respectively, and is thought to be subsequently degraded. The localization of this protein suggests that it may play a role in chromosome segregation during mitotis. It is thought to form either a homodimer or heterodimer. Autoantibodies against this protein have been found in patients with cancer or graft versus host disease. [provided by RefSeq, Jul 2008].  ",null,"C1855705","0/0","199,0","0","199","0/1","224,15","0.0628","239",null,"chr1:214630637:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CENPF","chr1:214630637","CENPF(N433S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Stromme syndrome (STROMS) [MIM:243605]: An autosomal recessive congenital disorder characterized by intestinal atresia, ocular anomalies, microcephaly, and renal and cardiac abnormalities in some patients. The disease has features of a ciliopathy, and lethality in early childhood is observed in severe cases. {ECO:0000269|PubMed:25564561, ECO:0000269|PubMed:26820108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for kinetochore function and chromosome segregation in mitosis. Required for kinetochore localization of dynein, LIS1, NDE1 and NDEL1. Regulates recycling of the plasma membrane by acting as a link between recycling vesicles and the microtubule network though its association with STX4 and SNAP25. Acts as a potential inhibitor of pocket protein-mediated cellular processes during development by regulating the activity of RB proteins during cell division and proliferation. May play a regulatory or permissive role in the normal embryonic cardiomyocyte cell cycle and in promoting continued mitosis in transformed, abnormally dividing neonatal cardiomyocytes. Interaction with RB directs embryonic stem cells toward a cardiac lineage. Involved in the regulation of DNA synthesis and hence cell cycle progression, via its C-terminus. Has a potential role regulating skeletal myogenesis and in cell differentiation in embryogenesis. Involved in dendritic cell regulation of T-cell immunity against chlamydia. {ECO:0000269|PubMed:12974617, ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:7542657, ECO:0000269|PubMed:7651420}.; ",{"$nulls":4},"p.Asn433Ser","c.1298A>G","MODERATE","433/3114",9,{"$nulls":5},"3","204","224",{"$nulls":4},"0","0",{"$nulls":22},"0.897834","-1.11",null,"1","-2.73","0.852","0.08","0.171",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein that associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. In late G2 the protein associates with the kinetochore and maintains this association through early anaphase. It localizes to the spindle midzone and the intracellular bridge in late anaphase and telophase, respectively, and is thought to be subsequently degraded. The localization of this protein suggests that it may play a role in chromosome segregation during mitotis. It is thought to form either a homodimer or heterodimer. Autoantibodies against this protein have been found in patients with cancer or graft versus host disease. [provided by RefSeq, Jul 2008].  ",null,"C1855705","0/0","186,0","0","186","0/1","198,12","0.0571","210",null,"chr1:214630637:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CENPV","chr17:16353358","CENPV(S27P)",null,null,"compositionally biased region (Poly-Ala ), splice variant (In isoform 2. )",{"$nulls":3},58,"PASS","Missense","rs754483275",0.0001937,null,"FUNCTION: Required for distribution of pericentromeric heterochromatin in interphase nuclei and for centromere formation and organization, chromosome alignment and cytokinesis. {ECO:0000269|PubMed:18772885}.; ",{"$nulls":4},"p.Ser27Pro","c.79T>C","MODERATE","27/272",1,13,{"$nulls":4},"1",{"$nulls":30},"0.975153",null,null,"1;0.999857","0.19",null,"0.022","0.069",{"$nulls":3},"ExAC_AF",0.0001937,{"$nulls":7},"0/0","28,0","0","28","0/1","15,3","0.1667","18",null,"chr17:16353358:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1667"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CEP170","chr1:243191282","CEP170(I282F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in microtubule organization (PubMed:15616186). Required for centriole subdistal appendage assembly (PubMed:28422092). {ECO:0000269|PubMed:15616186, ECO:0000269|PubMed:28422092}.; ",{"$nulls":4},"p.Ile282Phe","c.844A>T","MODERATE","282/1584",8,{"$nulls":5},"2",null,null,"657","903",{"$nulls":26},"3.964719","1.43","3.4","0.999999","-3.9;-3.97;-3.97","0.999;0.999;1.0","0.0;0.001;0.0","0.742;0.72;0.77",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","801,0","0","803","0/1","717,396","0.3558","1115",null,"chr1:243191282:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3566"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CEP78","chr9:78251950","CEP78(S372C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Cone-rod dystrophy and hearing loss (CRDHL) [MIM:617236]: An autosomal recessive disease defined by the association of progressive cone-rod dystrophy with sensorineural hearing loss. Cone-rod dystrophy is characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:27588451, ECO:0000269|PubMed:27588452, ECO:0000269|PubMed:27627988}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be required for efficient PLK4 centrosomal localization and PLK4-induced overduplication of centrioles (PubMed:27246242). May play a role in cilium biogenesis (PubMed:27588451). {ECO:0000269|PubMed:27246242, ECO:0000269|PubMed:27588451}.; ",{"$nulls":4},"p.Ser372Cys","c.1115C>G","MODERATE","372/722",9,{"$nulls":5},"5","284","277","191","195","234","240","0","0","0","0.1375",{"$nulls":20},"1.012928","1.64;.;.;.;.;.;.;1.82;1.61;1.64;.;.;.;.","0.92;.;.;.;.;.;0.92;.;.;.;.;.;.;.","1","-1.55;.;.;.;.;.;.;-1.47;-1.65;-1.51;.;.;.;.","0.002;.;.;.;.;.;.;.;0.003;.;.;.;.;.","0.096;.;.;.;.;.;.;0.088;0.082;0.097;.;.;.;.","0.151;.;.;.;.;.;.;0.144;0.141;0.152;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193018","0/0","273,0","0","273","0/1","226,35","0.1341","261",null,"chr9:78251950:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1231"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CEP95","chr17:64519428","CEP95(R194T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg194Thr","c.581G>C","MODERATE","194/821",6,{"$nulls":5},"4","263","299","187","194","254","272","0","0","0","0.4044",{"$nulls":20},"4.122271","1.03;0.23;.","2.455;.;.","0.999918","-3.29;.;.","1.0;.;.","0.0;.;.","0.52;.;0.378",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","262,0","0","262","0/1","174,122","0.4122","296",null,"chr17:64519428:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3969"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CEP95","chr17:64519428","CEP95(R194T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg194Thr","c.581G>C","MODERATE","194/821",6,{"$nulls":5},"4","263","298","187","207","254","276","0","0","0","0.1522",{"$nulls":20},"4.122271","1.03;0.23;.","2.455;.;.","0.999918","-3.29;.;.","1.0;.;.","0.0;.;.","0.52;.;0.378",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","262,0","0","262","0/1","239,50","0.173","289",null,"chr17:64519428:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1546"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CGNL1","chr15:57439475","CGNL1(K492N)",null,null,"region of interest (Head ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Aromatase excess syndrome (AEXS) [MIM:139300]: An autosomal dominant disorder characterized by increased extraglandular aromatization of steroids that presents with heterosexual precocity in males and isosexual precocity in females. {ECO:0000269|PubMed:12736278}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration inv(15)(q21.2;q21.3) has been found in patients with aromatase excess syndrome. The inversion moves the promoter of the CGNL1 gene into a 5-prime position in relation to the aromatase coding region.; ","FUNCTION: May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons. {ECO:0000269|PubMed:22891260}.; ",{"$nulls":4},"p.Lys492Asn","c.1476A>C","MODERATE","492/1302",2,{"$nulls":5},"4","259","242","215","193","233","217","0","0","0","0.2212",{"$nulls":20},"1.111994","-1.25","1.935","0.990925","-1.82","0.411","0.109","0.202",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the cingulin family. The encoded protein localizes to both adherens and tight cell-cell junctions and mediates junction assembly and maintenance by regulating the activity of the small GTPases RhoA and Rac1. Heterozygous chromosomal rearrangements resulting in association of the promoter for this gene with the aromatase gene are a cause of aromatase excess syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011].",null,null,"0/0","248,1","0.004","249","0/1","188,51","0.2134","239",null,"chr15:57439475:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2124"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CGNL1","chr15:57439475","CGNL1(K492N)",null,null,"region of interest (Head ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Aromatase excess syndrome (AEXS) [MIM:139300]: An autosomal dominant disorder characterized by increased extraglandular aromatization of steroids that presents with heterosexual precocity in males and isosexual precocity in females. {ECO:0000269|PubMed:12736278}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration inv(15)(q21.2;q21.3) has been found in patients with aromatase excess syndrome. The inversion moves the promoter of the CGNL1 gene into a 5-prime position in relation to the aromatase coding region.; ","FUNCTION: May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons. {ECO:0000269|PubMed:22891260}.; ",{"$nulls":4},"p.Lys492Asn","c.1476A>C","MODERATE","492/1302",2,{"$nulls":5},"4","259","292","215","234","235","262","0","0","0","0.0954",{"$nulls":20},"1.111994","-1.25","1.935","0.990925","-1.82","0.411","0.109","0.202",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the cingulin family. The encoded protein localizes to both adherens and tight cell-cell junctions and mediates junction assembly and maintenance by regulating the activity of the small GTPases RhoA and Rac1. Heterozygous chromosomal rearrangements resulting in association of the promoter for this gene with the aromatase gene are a cause of aromatase excess syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011].",null,null,"0/0","248,1","0.004","249","0/1","259,28","0.0976","287",null,"chr15:57439475:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1026"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CHI3L1","chr1:203179458","CHI3L1(L380H)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Asthma-related traits 7 (ASRT7) [MIM:611960]: Asthma- related traits include clinical symptoms of asthma, such as coughing, wheezing, dyspnea, bronchial hyperresponsiveness as assessed by methacholine challenge test, serum IgE levels, atopy and atopic dermatitis. {ECO:0000269|PubMed:18403759}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:17160890, ECO:0000269|PubMed:20051317}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Carbohydrate-binding lectin with a preference for chitin. Has no chitinase activity. May play a role in tissue remodeling and in the capacity of cells to respond to and cope with changes in their environment. Plays a role in T-helper cell type 2 (Th2) inflammatory response and IL-13-induced inflammation, regulating allergen sensitization, inflammatory cell apoptosis, dendritic cell accumulation and M2 macrophage differentiation. Facilitates invasion of pathogenic enteric bacteria into colonic mucosa and lymphoid organs. Mediates activation of AKT1 signaling pathway and subsequent IL8 production in colonic epithelial cells. Regulates antibacterial responses in lung by contributing to macrophage bacterial killing, controlling bacterial dissemination and augmenting host tolerance. Also regulates hyperoxia-induced injury, inflammation and epithelial apoptosis in lung. {ECO:0000269|PubMed:16472595, ECO:0000269|PubMed:19414556, ECO:0000269|PubMed:20558631, ECO:0000269|PubMed:9492324}.; ",{"$nulls":5},"c.1139T>A","HIGH",null,10,{"$nulls":5},"5","911","1060","680","800","753","850","0","0","0","0.1847",{"$nulls":20},"3.532908","1.14","4.55","0.954349","-6.07","1.0",null,"0.636",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0036341| C2677770","0/0","846,0","0","846","0/1","847,155","0.1547","1002",null,"chr1:203179458:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1613"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CHI3L1","chr1:203179458","CHI3L1(L380H)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Asthma-related traits 7 (ASRT7) [MIM:611960]: Asthma- related traits include clinical symptoms of asthma, such as coughing, wheezing, dyspnea, bronchial hyperresponsiveness as assessed by methacholine challenge test, serum IgE levels, atopy and atopic dermatitis. {ECO:0000269|PubMed:18403759}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:17160890, ECO:0000269|PubMed:20051317}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Carbohydrate-binding lectin with a preference for chitin. Has no chitinase activity. May play a role in tissue remodeling and in the capacity of cells to respond to and cope with changes in their environment. Plays a role in T-helper cell type 2 (Th2) inflammatory response and IL-13-induced inflammation, regulating allergen sensitization, inflammatory cell apoptosis, dendritic cell accumulation and M2 macrophage differentiation. Facilitates invasion of pathogenic enteric bacteria into colonic mucosa and lymphoid organs. Mediates activation of AKT1 signaling pathway and subsequent IL8 production in colonic epithelial cells. Regulates antibacterial responses in lung by contributing to macrophage bacterial killing, controlling bacterial dissemination and augmenting host tolerance. Also regulates hyperoxia-induced injury, inflammation and epithelial apoptosis in lung. {ECO:0000269|PubMed:16472595, ECO:0000269|PubMed:19414556, ECO:0000269|PubMed:20558631, ECO:0000269|PubMed:9492324}.; ",{"$nulls":5},"c.1139T>A","HIGH",null,10,{"$nulls":5},"5","911","1101","680","832","754","884","0","0","0","0.095",{"$nulls":20},"3.532908","1.14","4.55","0.954349","-6.07","1.0",null,"0.636",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0036341| C2677770","0/0","862,0","0","862","0/1","973,88","0.0829","1061",null,"chr1:203179458:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0781"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CHMP2B","chr3:87240739","CHMP2B(Q25H)",null,null,"coiled-coil region , splice variant (In isoform 2. )","coiled-coil-region:match_to_sequence_model_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Frontotemporal dementia, chromosome 3-linked (FTD3) [MIM:600795]: Characterized by an onset of dementia in the late 50's initially characterized by behavioral and personality changes including apathy, restlessness, disinhibition and hyperorality, progressing to stereotyped behaviors, non-fluent aphasia, mutism and dystonia, with a marked lack of insight. The brains of individuals with FTD3 have no distinctive neuropathological features. They show global cortical and central atrophy, but no beta-amyloid deposits. {ECO:0000269|PubMed:16041373}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Amyotrophic lateral sclerosis 17 (ALS17) [MIM:614696]: An adult-onset progressive neurodegenerative disorder with predominantly lower motor neuron involvement, manifest as muscle weakness and wasting of the upper and lower limbs, bulbar signs, and respiratory insufficiency. {ECO:0000269|PubMed:16807408, ECO:0000269|PubMed:20352044}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4.; ",{"$nulls":4},"p.Gln25His","c.75G>T","MODERATE","25/213",2,{"$nulls":5},"5","193","202","138","136","178","179","0","0","0","0.2067",{"$nulls":20},"2.586983","-0.67;-0.67;.","3.035;.;.","0.999999;0.999999;1","-1.73;-1.7;.","0.006;.;.","0.164;0.168;.","0.841;0.833;.",{"$nulls":3},"Unknown",-1,"AD","Amyotrophic lateral sclerosis, CHMP2B-related; Dementia, familial, nonspecific; Frontotemporal dementia, chromosome 3-linked ","Neurologic",{"$nulls":3},"C1836076| C1833296","0/0","191,0","0","191","0/1","152,41","0.2124","193",null,"chr3:87240739:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1985"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CHMP2B","chr3:87240739","CHMP2B(Q25H)",null,null,"coiled-coil region , splice variant (In isoform 2. )","coiled-coil-region:match_to_sequence_model_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Frontotemporal dementia, chromosome 3-linked (FTD3) [MIM:600795]: Characterized by an onset of dementia in the late 50's initially characterized by behavioral and personality changes including apathy, restlessness, disinhibition and hyperorality, progressing to stereotyped behaviors, non-fluent aphasia, mutism and dystonia, with a marked lack of insight. The brains of individuals with FTD3 have no distinctive neuropathological features. They show global cortical and central atrophy, but no beta-amyloid deposits. {ECO:0000269|PubMed:16041373}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Amyotrophic lateral sclerosis 17 (ALS17) [MIM:614696]: An adult-onset progressive neurodegenerative disorder with predominantly lower motor neuron involvement, manifest as muscle weakness and wasting of the upper and lower limbs, bulbar signs, and respiratory insufficiency. {ECO:0000269|PubMed:16807408, ECO:0000269|PubMed:20352044}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4.; ",{"$nulls":4},"p.Gln25His","c.75G>T","MODERATE","25/213",2,{"$nulls":5},"5","193","243","138","169","178","217","0","0","0","0.0922",{"$nulls":20},"2.586983","-0.67;-0.67;.","3.035;.;.","0.999999;0.999999;1","-1.73;-1.7;.","0.006;.;.","0.164;0.168;.","0.841;0.833;.",{"$nulls":3},"Unknown",-1,"AD","Amyotrophic lateral sclerosis, CHMP2B-related; Dementia, familial, nonspecific; Frontotemporal dementia, chromosome 3-linked ","Neurologic",{"$nulls":3},"C1836076| C1833296","0/0","190,0","0","190","0/1","206,26","0.1121","232",null,"chr3:87240739:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1124"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CHP2","chr16:23756161","CHP2(E107A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as an integral cofactor in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity. Binds to and activates SLC9A1/NHE1 in a serum-independent manner, thus increasing pH and protecting cells from serum deprivation- induced death. Also plays a role in the regulation of cell proliferation and tumor growth by increasing the phosphatase activity of PPP3CA in a calcium-dependent manner. Activator of the calcineurin/NFAT signaling pathway. Involved in the cytoplasmic translocation of the transcription factor NFATC3 to the nucleus. {ECO:0000269|PubMed:12226101, ECO:0000269|PubMed:18815128}.; ","level2",{"$nulls":3},"p.Glu107Ala","c.320A>C","MODERATE","107/196",4,{"$nulls":5},"5","189","237","134","174","172","226","0","0","0","0.1637",{"$nulls":20},"2.659446","-0.69","2.62","0.994481","-2.82","0.304","0.277","0.392",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS,kMAPK,kVEGF,kWNT",{"$nulls":3},"0/0","179,0","0","179","0/1","201,38","0.159","239",null,"chr16:23756161:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1724"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CHP2","chr16:23756161","CHP2(E107A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as an integral cofactor in cell pH regulation by controlling plasma membrane-type Na(+)/H(+) exchange activity. Binds to and activates SLC9A1/NHE1 in a serum-independent manner, thus increasing pH and protecting cells from serum deprivation- induced death. Also plays a role in the regulation of cell proliferation and tumor growth by increasing the phosphatase activity of PPP3CA in a calcium-dependent manner. Activator of the calcineurin/NFAT signaling pathway. Involved in the cytoplasmic translocation of the transcription factor NFATC3 to the nucleus. {ECO:0000269|PubMed:12226101, ECO:0000269|PubMed:18815128}.; ","level2",{"$nulls":3},"p.Glu107Ala","c.320A>C","MODERATE","107/196",4,{"$nulls":5},"5","189","221","134","162","171","199","0","0","0","0.0553",{"$nulls":20},"2.659446","-0.69","2.62","0.994481","-2.82","0.304","0.277","0.392",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS,kMAPK,kVEGF,kWNT",{"$nulls":3},"0/0","179,0","0","179","0/1","202,16","0.0734","218",null,"chr16:23756161:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0741"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CIC","chr19:42272892","CIC(P371fs)",null,null,"sequence variant (In MRD45; decreased protein expression. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcriptional repressor which plays a role in development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, involved in brain development. {ECO:0000250|UniProtKB:Q924A2}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Pro371fs","c.1112delC","HIGH","371/2514",2,{"$nulls":5},"5","415","429","327","344","364","368","0","0","0","0.1304",{"$nulls":5},"(CIC|ENSG00000079432|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"COSMIC",null,null,"C4539848","0/0","392,0","0","392","0/1","350,52","0.1294","402",null,"chr19:42272892:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1337"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CIC","chr19:42272892","CIC(P371fs)",null,null,"sequence variant (In MRD45; decreased protein expression. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcriptional repressor which plays a role in development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, involved in brain development. {ECO:0000250|UniProtKB:Q924A2}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Pro371fs","c.1112delC","HIGH","371/2514",2,{"$nulls":5},"4",null,null,"327","382","364","436",null,null,"0","0.0505",{"$nulls":5},"(CIC|ENSG00000079432|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"COSMIC",null,null,"C4539848","0/0","392,0","0","392","0/1","453,26","0.0543","479",null,"chr19:42272892:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.055"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CITED1","chrX:72301844","CITED1(D180V)",null,null,"compositionally biased region (Asp/Glu-rich (acidic) )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional coactivator of the p300/CBP-mediated transcription complex. Enhances SMAD-mediated transcription by strengthening the functional link between the DNA-binding SMAD transcription factors and the p300/CBP transcription coactivator complex. Stimulates estrogen-dependent transactivation activity mediated by estrogen receptors signaling; stabilizes the interaction of estrogen receptor ESR1 and histone acetyltransferase EP300. Positively regulates TGF-beta signaling through its association with the SMAD/p300/CBP-mediated transcriptional coactivator complex. Induces transcription from estrogen-responsive promoters and protection against cell death. Potentiates EGR2-mediated transcriptional activation activity from the ERBB2 promoter. Acts as an inhibitor of osteoblastic mineralization through a cAMP-dependent parathyroid hormone receptor signaling. May play a role in pigmentation of melanocytes. Associates with chromatin to the estrogen-responsive TGF-alpha promoter region in a estrogen-dependent manner. {ECO:0000269|PubMed:10722728, ECO:0000269|PubMed:11581164, ECO:0000269|PubMed:21172805}.; ",{"$nulls":4},"p.Asp180Val","c.539A>T","MODERATE","180/219",4,{"$nulls":5},"5","555","505","397","363","495","459","0","0","0","0.2113",{"$nulls":20},"4.03561","-1.49;-1.49;-1.49;-1.49;-1.49;.",".;.;2.56;2.56;2.56;.","0.999999","-8.61;-8.61;-8.58;-8.58;-8.58;.","1.0;1.0;1.0;1.0;1.0;.","0.0;0.0;0.0;0.0;0.0;.","0.853;0.852;0.846;0.847;0.846;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","547,0","0","547","0/1","384,100","0.2066","484",null,"chrX:72301844:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2039"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CITED1","chrX:72301844","CITED1(D180V)",null,null,"compositionally biased region (Asp/Glu-rich (acidic) )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional coactivator of the p300/CBP-mediated transcription complex. Enhances SMAD-mediated transcription by strengthening the functional link between the DNA-binding SMAD transcription factors and the p300/CBP transcription coactivator complex. Stimulates estrogen-dependent transactivation activity mediated by estrogen receptors signaling; stabilizes the interaction of estrogen receptor ESR1 and histone acetyltransferase EP300. Positively regulates TGF-beta signaling through its association with the SMAD/p300/CBP-mediated transcriptional coactivator complex. Induces transcription from estrogen-responsive promoters and protection against cell death. Potentiates EGR2-mediated transcriptional activation activity from the ERBB2 promoter. Acts as an inhibitor of osteoblastic mineralization through a cAMP-dependent parathyroid hormone receptor signaling. May play a role in pigmentation of melanocytes. Associates with chromatin to the estrogen-responsive TGF-alpha promoter region in a estrogen-dependent manner. {ECO:0000269|PubMed:10722728, ECO:0000269|PubMed:11581164, ECO:0000269|PubMed:21172805}.; ",{"$nulls":4},"p.Asp180Val","c.539A>T","MODERATE","180/219",4,{"$nulls":5},"5","555","653","397","441","494","585","0","0","0","0.0855",{"$nulls":20},"4.03561","-1.49;-1.49;-1.49;-1.49;-1.49;.",".;.;2.56;2.56;2.56;.","0.999999","-8.61;-8.61;-8.58;-8.58;-8.58;.","1.0;1.0;1.0;1.0;1.0;.","0.0;0.0;0.0;0.0;0.0;.","0.853;0.852;0.846;0.847;0.846;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","546,0","0","546","0/1","578,56","0.0883","634",null,"chrX:72301844:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0884"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CLEC4C","chr12:7729673","CLEC4C(E189K)",null,null,"topological domain (Extracellular ), domain (C-type lectin ), disulfide bond , disulfide bond , turn ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Lectin-type cell surface receptor which may play a role in antigen capturing by dendritic cells (PubMed:11748283, PubMed:21880719, PubMed:25995448). Specifically recognizes non- sialylated galactose-terminated biantennary glycans containing the trisaccharide epitope Gal(beta1-3/4)GlcNAc(beta1-2)Man (PubMed:21880719, PubMed:25995448). Binds to serum IgG (PubMed:25995448). Efficiently targets ligand into antigen- processing and peptide-loading compartments for presentation to T- cells (PubMed:11748283). May mediate potent inhibition of induction of IFN-alpha/beta expression in plasmacytoid dendritic cells (PubMed:11748283, PubMed:21880719). May act as a signaling receptor that activates protein-tyrosine kinases and mobilizes intracellular calcium (PubMed:11748283). {ECO:0000269|PubMed:11748283, ECO:0000269|PubMed:21880719, ECO:0000269|PubMed:25995448}.; ",{"$nulls":4},"p.Glu189Lys","c.565G>A","MODERATE","189/213",6,{"$nulls":5},"5","642","500","430","337","598","460","0","0","0","0.0783",{"$nulls":20},"-0.105568","2.24","0.31;.;.;0.31","1","0.68;0.89;0.89;0.68","0.043;0.0;0.0;0.043","0.919;0.986;0.986;0.919","0.104;0.116;0.122;0.101",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","621,0","0","621","0/1","429,44","0.093","473",null,"chr12:7729673:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1039"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CLIP3","chr19:36024407","CLIP3(D303H)",null,null,"turn ","turn:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes. {ECO:0000269|PubMed:19139280}.; ",{"$nulls":4},"p.Asp303His","c.907G>C","MODERATE","303/547",7,{"$nulls":5},"5","502","501","367","362","342","327","0","0","0","0.1162",{"$nulls":20},"3.431837","-2.86","2.375","1","-1.58;.","1.0","0.182;.","0.674;0.567",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","429,0","0","429","0/1","370,47","0.1127","417",null,"chr19:36024407:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.116"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CLIP3","chr19:36024407","CLIP3(D303H)",null,null,"turn ","turn:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes. {ECO:0000269|PubMed:19139280}.; ",{"$nulls":4},"p.Asp303His","c.907G>C","MODERATE","303/547",7,{"$nulls":5},"4",null,null,"367","419","345","368",null,null,"0","0.0897",{"$nulls":20},"3.431837","-2.86","2.375","1","-1.58;.","1.0","0.182;.","0.674;0.567",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","446,0","0","502","0/1","445,39","0.0806","551",null,"chr19:36024407:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0931"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CLNK","chr4:10558431","CLNK(D141Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the regulation of immunoreceptor signaling, including PLC-gamma-mediated B-cell antigen receptor (BCR) signaling and FC-epsilon R1-mediated mast cell degranulation. Involved in phosphorylation of LAT (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp141Tyr","c.421G>T","MODERATE","141/428",8,{"$nulls":5},"5","775","803","544","567","670","689","0","0","0","0.1205",{"$nulls":20},"3.247464","1.39;.;0.06","1.59;.;.","0.999994","-3.45;.;-5.62","0.999;.;1.0","0.001;.;0.006","0.536;0.532;0.762",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","722,0","0","722","0/1","660,91","0.1212","751",null,"chr4:10558431:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1111"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CLNK","chr4:10558431","CLNK(D141Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the regulation of immunoreceptor signaling, including PLC-gamma-mediated B-cell antigen receptor (BCR) signaling and FC-epsilon R1-mediated mast cell degranulation. Involved in phosphorylation of LAT (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp141Tyr","c.421G>T","MODERATE","141/428",8,{"$nulls":5},"3","775","935",{"$nulls":4},"0","0",{"$nulls":22},"3.247464","1.39;.;0.06","1.59;.;.","0.999994","-3.45;.;-5.62","0.999;.;1.0","0.001;.;0.006","0.536;0.532;0.762",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","730,0","0","730","0/1","828,49","0.0559","877",null,"chr4:10558431:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","COL4A6","chrX:108178836","COL4A6(G805E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS).; DISEASE: Deafness, X-linked, 6 (DFNX6) [MIM:300914]: A non- syndromic form of sensorineural hearing loss with prelingual onset. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:23714752}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.; ","level2",{"$nulls":3},"p.Gly805Glu","c.2414G>A","MODERATE","805/1707",28,{"$nulls":5},"5","348","433","248","313","310","379","0","0","0","0.3588",{"$nulls":20},"2.722622","-6.28;-6.28;.;-5.77;.;-5.77",".;3.54;.;.;.;.","0.999147","-7.37;-7.5;.;-7.32;.;-7.32","1.0;1.0;.;1.0;.;1.0","0.002;0.002;.;0.002;.;0.002","0.837;0.869;0.877;0.857;0.869;0.788",{"$nulls":3},"Unknown",-1,"XL","Deafness, X-linked, with cochlear malformation","Audiologic/Otolaryngologic","kCANCER",null,null,"C3806737","0/0","343,0","0","343","0/1","269,160","0.373","429",null,"chrX:108178836:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3546"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","COL4A6","chrX:108178836","COL4A6(G805E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS).; DISEASE: Deafness, X-linked, 6 (DFNX6) [MIM:300914]: A non- syndromic form of sensorineural hearing loss with prelingual onset. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:23714752}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.; ","level2",{"$nulls":3},"p.Gly805Glu","c.2414G>A","MODERATE","805/1707",28,{"$nulls":5},"5","348","351","248","238","309","303","0","0","0","0.1749",{"$nulls":20},"2.722622","-6.28;-6.28;.;-5.77;.;-5.77",".;3.54;.;.;.;.","0.999147","-7.37;-7.5;.;-7.32;.;-7.32","1.0;1.0;.;1.0;.;1.0","0.002;0.002;.;0.002;.;0.002","0.837;0.869;0.877;0.857;0.869;0.788",{"$nulls":3},"Unknown",-1,"XL","Deafness, X-linked, with cochlear malformation","Audiologic/Otolaryngologic","kCANCER",null,null,"C3806737","0/0","341,0","0","341","0/1","280,67","0.1931","347",null,"chrX:108178836:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1933"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","COLEC12","chr18:321684","COLEC12(I729M)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid-beta in Alzheimer disease. {ECO:0000269|PubMed:11162630, ECO:0000269|PubMed:11564734, ECO:0000269|PubMed:12761161, ECO:0000269|PubMed:15845541, ECO:0000269|PubMed:16868960}.; ",{"$nulls":5},"c.2187T>G","HIGH",null,9,{"$nulls":5},"4","435","423","325","319","353","363","0","0","0","0.1708",{"$nulls":20},"2.439438","1.69","2.87","0.999986","-1.21","0.116",null,"0.895",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","408,0","0","408","0/1","346,65","0.1582","411",null,"chr18:321684:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1536"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","COLEC12","chr18:321684","COLEC12(I729M)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Scavenger receptor that displays several functions associated with host defense. Promotes binding and phagocytosis of Gram-positive, Gram-negative bacteria and yeast. Mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. Binds to several carbohydrates including Gal-type ligands, D-galactose, L- and D-fucose, GalNAc, T and Tn antigens in a calcium-dependent manner and internalizes specifically GalNAc in nurse-like cells. Binds also to sialyl Lewis X or a trisaccharide and asialo-orosomucoid (ASOR). May also play a role in the clearance of amyloid-beta in Alzheimer disease. {ECO:0000269|PubMed:11162630, ECO:0000269|PubMed:11564734, ECO:0000269|PubMed:12761161, ECO:0000269|PubMed:15845541, ECO:0000269|PubMed:16868960}.; ",{"$nulls":5},"c.2187T>G","HIGH",null,9,{"$nulls":5},"4","435","499","325","381","355","424","0","0","0","0.0873",{"$nulls":20},"2.439438","1.69","2.87","0.999986","-1.21","0.116",null,"0.895",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","408,0","0","408","0/1","432,40","0.0847","472",null,"chr18:321684:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0892"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CPA5","chr7:130368429","CPA5(V382fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Val382fs","c.1144_1145delGT","HIGH","382/436",11,{"$nulls":5},"5","435","491","348","395","393","444","0","0","0","0.2117",{"$nulls":5},"(CPA5|ENSG00000158525|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","434,0","0","434","0/1","367,102","0.2175","469",null,"chr7:130368429:CGT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2127"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CPA5","chr7:130368429","CPA5(V382fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Val382fs","c.1144_1145delGT","HIGH","382/436",11,{"$nulls":5},"5","435","554","348","432","394","490","0","0","0","0.1388",{"$nulls":5},"(CPA5|ENSG00000158525|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","434,0","0","434","0/1","462,76","0.1413","538",null,"chr7:130368429:CGT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1458"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CPEB2","chr4:15003293","CPEB2(R207P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in translational regulation of stored mRNAs in transcriptionally inactive haploid spermatids. Binds to poly(U) RNA oligomers (By similarity). Required for cell cycle progression, specifically for the transition from metaphase to anaphase (PubMed:26398195). {ECO:0000250|UniProtKB:Q812E0, ECO:0000269|PubMed:26398195}.; ",{"$nulls":4},"p.Arg207Pro","c.620G>C","MODERATE","207/1034",1,{"$nulls":5},"5","143","123","105","88","121","102","0","0","0","0.1176",{"$nulls":20},"2.478335","0.57;0.59",null,"0.996002","-0.83",null,"0.0","0.256;0.235",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","138,0","0","138","0/1","105,16","0.1322","121",null,"chr4:15003293:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1591"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CPNE7","chr16:89585711","CPNE7(R311G)",{"$nulls":6},255,"PASS","Missense","rs760181647",-1,null,"FUNCTION: Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.; ",{"$nulls":4},"p.Arg311Gly","c.931C>G","MODERATE","311/633",9,{"$nulls":5},"5","405","266","287","173","348","208","0","0","0","0.1683",{"$nulls":20},"1.536341","1.12","-1.27;.","0.994363;0.990675","-0.76;-0.52","0.031;0.875","0.039;0.036","0.395;0.405",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the copine family, which is composed of calcium-dependent membrane-binding proteins. The gene product contains two N-terminal C2 domains and one von Willebrand factor A domain. The encoded protein may be involved in membrane trafficking. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008].",null,null,"0/0","378,0","0","378","0/1","198,44","0.1818","242",null,"chr16:89585711:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1908"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CPNE7","chr16:89585711","CPNE7(R311G)",{"$nulls":6},255,"PASS","Missense","rs760181647",-1,null,"FUNCTION: Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.; ",{"$nulls":4},"p.Arg311Gly","c.931C>G","MODERATE","311/633",9,{"$nulls":5},"5","405","357","287","222","346","269","0","0","0","0.0558",{"$nulls":20},"1.536341","1.12","-1.27;.","0.994363;0.990675","-0.76;-0.52","0.031;0.875","0.039;0.036","0.395;0.405",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the copine family, which is composed of calcium-dependent membrane-binding proteins. The gene product contains two N-terminal C2 domains and one von Willebrand factor A domain. The encoded protein may be involved in membrane trafficking. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008].",null,null,"0/0","390,0","0","390","0/1","313,22","0.0657","335",null,"chr16:89585711:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0766"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CSMD3","chr8:112263783","CSMD3(S3240T)",null,null,"topological domain (Extracellular ), domain (Sushi 25 ), disulfide bond , splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in dendrite development. {ECO:0000250|UniProtKB:Q80T79}.; ",{"$nulls":4},"p.Ser3240Thr","c.9718T>A","MODERATE","3240/3707",61,{"$nulls":5},"4","220","663","151","451","199","609","0","0","0","0.1248",{"$nulls":20},"2.893553","-0.18",".;0.555;.;.","0.971606;0.971606;0.971606;0.850771","-1.08","0.917;0.875;.;0.532","0.076;0.065;0.152;0.073","0.4;0.396;.;0.431",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","211,0","0","211","0/1","556,78","0.123","634",null,"chr8:112263783:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.122"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CWF19L1","chr10:100253428","CWF19L1(P206A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro206Ala","c.616C>G","MODERATE","206/538",6,{"$nulls":5},"5","391","321","312","264","318","249","0","0","0","0.1767",{"$nulls":20},"3.9457560000000003","1.23;.","3.24;.","0.999999","-7.15;.","1.0;.","0.0;.","0.945;.",{"$nulls":3},"Unknown",-1,"AR","Spinocerebellar ataxia, autosomal recessive 17","Neurologic",{"$nulls":3},"C4015301","0/0","369,0","0","369","0/1","267,48","0.1524","315",null,"chr10:100253428:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1515"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CWF19L1","chr10:100253428","CWF19L1(P206A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro206Ala","c.616C>G","MODERATE","206/538",6,{"$nulls":5},"5","391","408","312","323","318","323","0","0","0","0.0805",{"$nulls":20},"3.9457560000000003","1.23;.","3.24;.","0.999999","-7.15;.","1.0;.","0.0;.","0.945;.",{"$nulls":3},"Unknown",-1,"AR","Spinocerebellar ataxia, autosomal recessive 17","Neurologic",{"$nulls":3},"C4015301","0/0","374,0","0","374","0/1","370,29","0.0727","399",null,"chr10:100253428:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0743"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CXorf57","chrX:106622672","CXorf57(S222C)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser222Cys","c.665C>G","MODERATE","222/855",2,{"$nulls":5},"4","291","363","220","275","227","278","0","0","0","0.1223",{"$nulls":20},"1.91405","0.83;0.83;0.87",null,"0.982625","-2.26;-2.11;-1.93",null,".;0.055;0.034","0.227;0.211;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0|0","281,0","0","281","0|1","321,34","0.0958","355",null,"chrX:106622672:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0873"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CXorf67","chrX:51407131","CXorf67(Q39E)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln39Glu","c.115C>G","MODERATE","39/503",1,{"$nulls":5},"5","480","564","358","401","398","489","0","0","0","0.1309",{"$nulls":20},"-0.696886","0.87",null,"1","-1.63","0.05","0.204","0.027",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","467,0","0","467","0/1","475,81","0.1457","556",null,"chrX:51407131:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1471"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CYP21A2","chr6:32038582","CYP21A2(Q54E)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense","rs1441984965",-1,"DISEASE: Adrenal hyperplasia 3 (AH3) [MIM:201910]: A form of congenital adrenal hyperplasia, a common recessive disease due to defective synthesis of cortisol. Congenital adrenal hyperplasia is characterized by androgen excess leading to ambiguous genitalia in affected females, rapid somatic growth during childhood in both sexes with premature closure of the epiphyses and short adult stature. Four clinical types: 'salt wasting' (SW, the most severe type), 'simple virilizing' (SV, less severely affected patients), with normal aldosterone biosynthesis, 'non-classic form' or late- onset (NC or LOAH) and 'cryptic' (asymptomatic). {ECO:0000269|PubMed:10051010, ECO:0000269|PubMed:10094562, ECO:0000269|PubMed:10198222, ECO:0000269|PubMed:10364682, ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10408778, ECO:0000269|PubMed:10408786, ECO:0000269|PubMed:10443693, ECO:0000269|PubMed:10496074, ECO:0000269|PubMed:10720040, ECO:0000269|PubMed:11232002, ECO:0000269|PubMed:11598371, ECO:0000269|PubMed:11600539, ECO:0000269|PubMed:11746135, ECO:0000269|PubMed:12213891, ECO:0000269|PubMed:12222711, ECO:0000269|PubMed:12788866, ECO:0000269|PubMed:12887291, ECO:0000269|PubMed:12915679, ECO:0000269|PubMed:1406699, ECO:0000269|PubMed:1406709, ECO:0000269|PubMed:14676460, ECO:0000269|PubMed:14715874, ECO:0000269|PubMed:1496017, ECO:0000269|PubMed:15110320, ECO:0000269|PubMed:15126570, ECO:0000269|PubMed:16046588, ECO:0000269|PubMed:1644925, ECO:0000269|PubMed:16984992, ECO:0000269|PubMed:18319307, ECO:0000269|PubMed:18381579, ECO:0000269|PubMed:18445671, ECO:0000269|PubMed:1864962, ECO:0000269|PubMed:1937474, ECO:0000269|PubMed:20080860, ECO:0000269|PubMed:2072928, ECO:0000269|PubMed:21169732, ECO:0000269|PubMed:22014889, ECO:0000269|PubMed:2303461, ECO:0000269|PubMed:27721825, ECO:0000269|PubMed:3038528, ECO:0000269|PubMed:3257825, ECO:0000269|PubMed:3260007, ECO:0000269|PubMed:3267225, ECO:0000269|PubMed:3497399, ECO:0000269|PubMed:3871526, ECO:0000269|PubMed:7749410, ECO:0000269|PubMed:8478006, ECO:0000269|PubMed:8485582, ECO:0000269|PubMed:8989258, ECO:0000269|PubMed:9067760, ECO:0000269|PubMed:9187661, ECO:0000269|PubMed:9497336, ECO:0000269|PubMed:9580109}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Specifically catalyzes the 21-hydroxylation of steroids. Required for the adrenal synthesis of mineralocorticoids and glucocorticoids (PubMed:22014889). {ECO:0000269|PubMed:22014889, ECO:0000269|PubMed:25855791, ECO:0000269|PubMed:27721825}.; ",{"$nulls":4},"p.Gln54Glu","c.160C>G","MODERATE","54/495",1,{"$nulls":5},"2",null,null,"110","105",{"$nulls":26},"1.13851","-0.28;.;-0.28;-0.28;-1.16;.",null,"1","-0.56;.;-1.35;-1.25;-0.8;.","0.722;0.722;.;.;.;0.722","0.091;.;0.08;0.039;0.047;.","0.187;.;.;.;0.136;.",{"$nulls":3},"Unknown",-1,"AR","Adrenal hyperplasia, congenital, due to 21-hydroxylase deficiency; Hyperandrogenism, nonclassic type, due to 21-hydroxylase deficiency","Cardiovascular; Endocrine; Genitourinary; Oncologic",{"$nulls":3},"C2936858","0/0","141,0","0","141","0/1","108,21","0.1628","129",null,"chr6:32038582:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1429"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CYSTM1","chr5:140194584","CYSTM1(G40E)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly40Glu","c.119G>A","MODERATE","40/97",2,{"$nulls":5},"2","624","518",{"$nulls":4},"0.0016","0.0016",{"$nulls":22},"3.448014","-0.19;.",null,"0.999687","-4.79;.","1.0;.","0.111;.","0.793;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","585,1","0.0017","586","0/1","405,89","0.1802","494",null,"chr5:140194584:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","CYTIP","chr2:157416032","CYTIP(S242T)",null,null,"compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: By its binding to cytohesin-1 (CYTH1), it modifies activation of ARFs by CYTH1 and its precise function may be to sequester CYTH1 in the cytoplasm.; ",{"$nulls":4},"p.Ser242Thr","c.725G>C","MODERATE","242/359",8,{"$nulls":5},"5","239","381","206","312","199","339","0","0","0","0.1062",{"$nulls":20},"3.242222","1.9","2.495","0.999622;0.999943","-1.67","0.999","0.007","0.424",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","229,0","0","229","0/1","331,41","0.1102","372",null,"chr2:157416032:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1026"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","CYTIP","chr2:157416032","CYTIP(S242T)",null,null,"compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: By its binding to cytohesin-1 (CYTH1), it modifies activation of ARFs by CYTH1 and its precise function may be to sequester CYTH1 in the cytoplasm.; ",{"$nulls":4},"p.Ser242Thr","c.725G>C","MODERATE","242/359",8,{"$nulls":5},"5","239","373","206","308","199","320","0","0","0","0.0625",{"$nulls":20},"3.242222","1.9","2.495","0.999622;0.999943","-1.67","0.999","0.007","0.424",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","235,0","0","235","0/1","347,21","0.0571","368",null,"chr2:157416032:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0649"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DALRD3","chr3:49017705","DALRD3(S209Y)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser209Tyr","c.626C>A","MODERATE","209/543",3,{"$nulls":5},"4","557","466","424","352","488","401","0","0","0","0.3167",{"$nulls":20},"2.003734","0.83;0.87;0.81;0.86;0.87;.","0.895;0.895;.;.;.;.","1","-1.76;-1.88;-1.93;-1.76;-2.44;.","0.681;0.761;0.838;.;.;.","0.011;0.011;0.041;0.024;0.016;.","0.191;0.163;0.192;0.112;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN282591","0/0","543,0","0","543","0/1","316,144","0.313","460",null,"chr3:49017705:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.304"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DALRD3","chr3:49017705","DALRD3(S209Y)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser209Tyr","c.626C>A","MODERATE","209/543",3,{"$nulls":5},"4","557","629","424","481","490","550","0","0","0","0.1309",{"$nulls":20},"2.003734","0.83;0.87;0.81;0.86;0.87;.","0.895;0.895;.;.;.;.","1","-1.76;-1.88;-1.93;-1.76;-2.44;.","0.681;0.761;0.838;.;.;.","0.011;0.011;0.041;0.024;0.016;.","0.191;0.163;0.192;0.112;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN282591","0/0","542,0","0","542","0/1","531,83","0.1352","614",null,"chr3:49017705:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1455"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DAPK3","chr19:3969719","DAPK3(Q6R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine kinase which is involved in the regulation of apoptosis, autophagy, transcription, translation and actin cytoskeleton reorganization. Involved in the regulation of smooth muscle contraction. Regulates both type I (caspase- dependent) apoptotic and type II (caspase-independent) autophagic cell deaths signal, depending on the cellular setting. Involved in regulation of starvation-induced autophagy. Regulates myosin phosphorylation in both smooth muscle and non-muscle cells. In smooth muscle, regulates myosin either directly by phosphorylating MYL12B and MYL9 or through inhibition of smooth muscle myosin phosphatase (SMPP1M) via phosphorylation of PPP1R12A; the inhibition of SMPP1M functions to enhance muscle responsiveness to Ca(2+) and promote a contractile state. Phosphorylates MYL12B in non-muscle cells leading to reorganization of actin cytoskeleton. Isoform 2 can phosphorylate myosin, PPP1R12A and MYL12B. Overexpression leads to condensation of actin stress fibers into thick bundles. Involved in actin filament focal adhesion dynamics. The function in both reorganization of actin cytoskeleton and focal adhesion dissolution is modulated by RhoD. Positively regulates canonical Wnt/beta-catenin signaling through interaction with NLK and TCF7L2. Phosphorylates RPL13A on 'Ser-77' upon interferon-gamma activation which is causing RPL13A release from the ribosome, RPL13A association with the GAIT complex and its subsequent involvement in transcript-selective translation inhibition. Enhances transcription from AR-responsive promoters in a hormone- and kinase-dependent manner. Involved in regulation of cell cycle progression and cell proliferation. May be a tumor suppressor. {ECO:0000269|PubMed:10356987, ECO:0000269|PubMed:11384979, ECO:0000269|PubMed:11781833, ECO:0000269|PubMed:12917339, ECO:0000269|PubMed:15096528, ECO:0000269|PubMed:15367680, ECO:0000269|PubMed:16219639, ECO:0000269|PubMed:17126281, ECO:0000269|PubMed:17158456, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:18995835, ECO:0000269|PubMed:21169990, ECO:0000269|PubMed:21408167, ECO:0000269|PubMed:21454679, ECO:0000269|PubMed:21487036, ECO:0000269|PubMed:23454120}.; ","level2",{"$nulls":3},"p.Gln6Arg","c.17A>G","MODERATE","6/454",1,{"$nulls":5},"4","298","149","183","94","274","129","0","0","0","0.155",{"$nulls":20},"3.285975","1.12;1.12;0.03;0.03;-0.04","0.87;0.87;.;.;.","0.99938","-2.23;-2.23;.;.;.","0.433;0.433;.;.;.","0.012;0.012;.;.;.","0.667;0.665;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER",{"$nulls":3},"0/0","287,0","0","287","0/1","122,22","0.1528","144",null,"chr19:3969719:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1596"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DAPK3","chr19:3969719","DAPK3(Q6R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine kinase which is involved in the regulation of apoptosis, autophagy, transcription, translation and actin cytoskeleton reorganization. Involved in the regulation of smooth muscle contraction. Regulates both type I (caspase- dependent) apoptotic and type II (caspase-independent) autophagic cell deaths signal, depending on the cellular setting. Involved in regulation of starvation-induced autophagy. Regulates myosin phosphorylation in both smooth muscle and non-muscle cells. In smooth muscle, regulates myosin either directly by phosphorylating MYL12B and MYL9 or through inhibition of smooth muscle myosin phosphatase (SMPP1M) via phosphorylation of PPP1R12A; the inhibition of SMPP1M functions to enhance muscle responsiveness to Ca(2+) and promote a contractile state. Phosphorylates MYL12B in non-muscle cells leading to reorganization of actin cytoskeleton. Isoform 2 can phosphorylate myosin, PPP1R12A and MYL12B. Overexpression leads to condensation of actin stress fibers into thick bundles. Involved in actin filament focal adhesion dynamics. The function in both reorganization of actin cytoskeleton and focal adhesion dissolution is modulated by RhoD. Positively regulates canonical Wnt/beta-catenin signaling through interaction with NLK and TCF7L2. Phosphorylates RPL13A on 'Ser-77' upon interferon-gamma activation which is causing RPL13A release from the ribosome, RPL13A association with the GAIT complex and its subsequent involvement in transcript-selective translation inhibition. Enhances transcription from AR-responsive promoters in a hormone- and kinase-dependent manner. Involved in regulation of cell cycle progression and cell proliferation. May be a tumor suppressor. {ECO:0000269|PubMed:10356987, ECO:0000269|PubMed:11384979, ECO:0000269|PubMed:11781833, ECO:0000269|PubMed:12917339, ECO:0000269|PubMed:15096528, ECO:0000269|PubMed:15367680, ECO:0000269|PubMed:16219639, ECO:0000269|PubMed:17126281, ECO:0000269|PubMed:17158456, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:18995835, ECO:0000269|PubMed:21169990, ECO:0000269|PubMed:21408167, ECO:0000269|PubMed:21454679, ECO:0000269|PubMed:21487036, ECO:0000269|PubMed:23454120}.; ","level2",{"$nulls":3},"p.Gln6Arg","c.17A>G","MODERATE","6/454",1,{"$nulls":5},"4","298","268","183","174","273","239","0","0","0","0.0795",{"$nulls":20},"3.285975","1.12;1.12;0.03;0.03;-0.04","0.87;0.87;.;.;.","0.99938","-2.23;-2.23;.;.;.","0.433;0.433;.;.;.","0.012;0.012;.;.;.","0.667;0.665;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER",{"$nulls":3},"0/0","291,0","0","291","0/1","236,24","0.0923","260",null,"chr19:3969719:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0977"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DBN1","chr5:177457502","DBN1(E673D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Drebrins might play some role in cell migration, extension of neuronal processes and plasticity of dendrites. Required for actin polymerization at immunological synapses (IS) and for CXCR4 recruitment to IS. {ECO:0000269|PubMed:20215400}.; ",{"$nulls":4},"p.Glu673Asp","c.2019G>T","MODERATE","673/695",15,{"$nulls":5},"5","573","440","420","311","513","382","0","0","0","0.3848",{"$nulls":20},"2.935569","-4.88","0.975;.;.","0.86314;0.86314;0.86314;0.990751;1","-1.09","0.999;0.999;.","0.0","0.467;0.495;0.525",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a cytoplasmic actin-binding protein thought to play a role in the process of neuronal growth. It is a member of the drebrin family of proteins that are developmentally regulated in the brain. A decrease in the amount of this protein in the brain has been implicated as a possible contributing factor in the pathogenesis of memory disturbance in Alzheimer's disease. At least two alternative splice variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008].",null,null,"0/0","536,0","0","536","0/1","250,158","0.3873","408",null,"chr5:177457502:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3762"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DBN1","chr5:177457502","DBN1(E673D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Drebrins might play some role in cell migration, extension of neuronal processes and plasticity of dendrites. Required for actin polymerization at immunological synapses (IS) and for CXCR4 recruitment to IS. {ECO:0000269|PubMed:20215400}.; ",{"$nulls":4},"p.Glu673Asp","c.2019G>T","MODERATE","673/695",15,{"$nulls":5},"5","573","587","420","431","513","506","0","0","0","0.1245",{"$nulls":20},"2.935569","-4.88","0.975;.;.","0.86314;0.86314;0.86314;0.990751;1","-1.09","0.999;0.999;.","0.0","0.467;0.495;0.525",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a cytoplasmic actin-binding protein thought to play a role in the process of neuronal growth. It is a member of the drebrin family of proteins that are developmentally regulated in the brain. A decrease in the amount of this protein in the brain has been implicated as a possible contributing factor in the pathogenesis of memory disturbance in Alzheimer's disease. At least two alternative splice variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008].",null,null,"0/0","551,0","0","551","0/1","484,78","0.1388","562",null,"chr5:177457502:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1369"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DCC","chr18:53157422","DCC(R443Q)",null,null,"topological domain (Extracellular ), domain (Fibronectin type-III 1 ), sequence variant (In MRMV1. )",{"$nulls":3},255,"PASS","Missense","rs200830938",9.9403578528827028E-4,"DISEASE: Mirror movements 1 (MRMV1) [MIM:157600]: A disorder characterized by contralateral involuntary movements that mirror voluntary ones. While mirror movements are occasionally found in young children, persistence beyond the age of 10 is abnormal. Mirror movements occur more commonly in the upper extremities. Some MRMV1 patients have agenesis of the corpus callosum. {ECO:0000269|PubMed:20431009, ECO:0000269|PubMed:28250454}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Gaze palsy, familial horizontal, with progressive scoliosis, 2 (HGPPS2) [MIM:617542]: An autosomal recessive neurologic disorder characterized by global developmental delay, delayed walking, intellectual disability, horizontal gaze palsy, and childhood-onset progressive scoliosis. {ECO:0000269|PubMed:28250456}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor for netrin required for axon guidance. Mediates axon attraction of neuronal growth cones in the developing nervous system upon ligand binding. Its association with UNC5 proteins may trigger signaling for axon repulsion. It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand. Implicated as a tumor suppressor gene. {ECO:0000269|PubMed:8187090, ECO:0000269|PubMed:8861902}.; ","gedi|level2",{"$nulls":3},"p.Arg443Gln","c.1328G>A","MODERATE","443/1447",8,4,{"$nulls":4},"5","716","797","473","556","634","706","0","0","0","0.3045",{"$nulls":20},"4.45497","0.4;.;0.4;0.25","2.34;.;.;.","0.999998","-3.49;.;.;.","1.0;.;.;.","0.0;.;.;.","0.867;.;0.886;.",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,"AD","Mirror movements 1","Neurologic","kCANCER","This gene encodes a netrin 1 receptor. The transmembrane protein is a member of the immunoglobulin superfamily of cell adhesion molecules, and mediates axon guidance of neuronal growth cones towards sources of netrin 1 ligand. The cytoplasmic tail interacts with the tyrosine kinases Src and focal adhesion kinase (FAK, also known as PTK2) to mediate axon attraction. The protein partially localizes to lipid rafts, and induces apoptosis in the absence of ligand. The protein functions as a tumor suppressor, and is frequently mutated or downregulated in colorectal cancer and esophageal carcinoma. [provided by RefSeq, Oct 2009].  ",null,"C1527249| C0546837| C4479640| C1834870","0/0","663,0","0","663","0/1","518,232","0.3093","750",null,"chr18:53157422:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3022"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DCC","chr18:53157422","DCC(R443Q)",null,null,"topological domain (Extracellular ), domain (Fibronectin type-III 1 ), sequence variant (In MRMV1. )",{"$nulls":3},255,"PASS","Missense","rs200830938",9.9403578528827028E-4,"DISEASE: Mirror movements 1 (MRMV1) [MIM:157600]: A disorder characterized by contralateral involuntary movements that mirror voluntary ones. While mirror movements are occasionally found in young children, persistence beyond the age of 10 is abnormal. Mirror movements occur more commonly in the upper extremities. Some MRMV1 patients have agenesis of the corpus callosum. {ECO:0000269|PubMed:20431009, ECO:0000269|PubMed:28250454}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Gaze palsy, familial horizontal, with progressive scoliosis, 2 (HGPPS2) [MIM:617542]: An autosomal recessive neurologic disorder characterized by global developmental delay, delayed walking, intellectual disability, horizontal gaze palsy, and childhood-onset progressive scoliosis. {ECO:0000269|PubMed:28250456}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor for netrin required for axon guidance. Mediates axon attraction of neuronal growth cones in the developing nervous system upon ligand binding. Its association with UNC5 proteins may trigger signaling for axon repulsion. It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand. Implicated as a tumor suppressor gene. {ECO:0000269|PubMed:8187090, ECO:0000269|PubMed:8861902}.; ","gedi|level2",{"$nulls":3},"p.Arg443Gln","c.1328G>A","MODERATE","443/1447",8,4,{"$nulls":4},"5","716","729","473","506","636","655","0","0","0","0.1527",{"$nulls":20},"4.45497","0.4;.;0.4;0.25","2.34;.;.;.","0.999998","-3.49;.;.;.","1.0;.;.;.","0.0;.;.;.","0.867;.;0.886;.",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,"AD","Mirror movements 1","Neurologic","kCANCER","This gene encodes a netrin 1 receptor. The transmembrane protein is a member of the immunoglobulin superfamily of cell adhesion molecules, and mediates axon guidance of neuronal growth cones towards sources of netrin 1 ligand. The cytoplasmic tail interacts with the tyrosine kinases Src and focal adhesion kinase (FAK, also known as PTK2) to mediate axon attraction. The protein partially localizes to lipid rafts, and induces apoptosis in the absence of ligand. The protein functions as a tumor suppressor, and is frequently mutated or downregulated in colorectal cancer and esophageal carcinoma. [provided by RefSeq, Oct 2009].  ",null,"C1527249| C0546837| C4479640| C1834870","0/0","678,0","0","678","0/1","588,107","0.154","695",null,"chr18:53157422:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1443"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DCHS2","chr4:154297901","DCHS2(S1683F)",null,null,"domain (Cadherin 14 ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium-dependent cell-adhesion protein. {ECO:0000250}.; ",{"$nulls":4},"p.Ser1683Phe","c.5048C>T","MODERATE","1683/2916",18,3,{"$nulls":4},"5","239","247","201","208","186","188","0","0","0","0.1755",{"$nulls":20},"3.42619",null,null,"0.537942",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","238,0","0","238","0/1","197,43","0.1792","240",null,"chr4:154297901:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1731"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DCHS2","chr4:154297901","DCHS2(S1683F)",null,null,"domain (Cadherin 14 ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium-dependent cell-adhesion protein. {ECO:0000250}.; ",{"$nulls":4},"p.Ser1683Phe","c.5048C>T","MODERATE","1683/2916",18,3,{"$nulls":4},"5","239","240","201","201","185","180","0","0","0","0.0944",{"$nulls":20},"3.42619",null,null,"0.537942",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","237,0","0","237","0/1","216,19","0.0809","235",null,"chr4:154297901:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0796"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DCLRE1A","chr10:113837136","DCLRE1A(G963A)",null,null,"strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be required for DNA interstrand cross-link repair. Also required for checkpoint mediated cell cycle arrest in early prophase in response to mitotic spindle poisons. {ECO:0000269|PubMed:15542852}.; ",{"$nulls":4},"p.Gly963Ala","c.2888G>C","MODERATE","963/1040",8,{"$nulls":5},"5","333","271","213","171","301","223","0","0","0","0.0942",{"$nulls":20},"3.769134","0.22","3.765","1","-5.83","0.997","0.0","0.867;0.866",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","327,0","0","327","0/1","229,34","0.1293","263",null,"chr10:113837136:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1404"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DDX41","chr5:177516910","DDX41(E3Q)",{"$nulls":6},255,"PASS","Missense","rs765022870",1.081E-4,"DISEASE: Myeloproliferative/lymphoproliferative neoplasms, familial (MPLPF) [MIM:616871]: A familial cancer predisposition syndrome with incomplete penetrance, characterized by increased susceptibility to myeloid neoplasms and rarely to lymphoid malignancies. MPLPF inheritance is autosomal dominant. {ECO:0000269|PubMed:25920683, ECO:0000269|PubMed:26712909}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:25920683}.; ",{"$nulls":4},"p.Glu3Gln","c.7G>C","MODERATE","3/640",1,{"$nulls":5},"3","74","56","51","36",null,null,"0","0",{"$nulls":22},"0.416756","1.63",null,"0.999993","0.06",{"$nulls":6},"ExAC_NFE_AF",1.081E-4,{"$nulls":6},"C4225174","0/0","69,0","0","69","0/1","39,16","0.2909","55",null,"chr5:177516910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2778"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DDX41","chr5:177516910","DDX41(E3Q)",{"$nulls":6},255,"PASS","Missense","rs765022870",1.081E-4,"DISEASE: Myeloproliferative/lymphoproliferative neoplasms, familial (MPLPF) [MIM:616871]: A familial cancer predisposition syndrome with incomplete penetrance, characterized by increased susceptibility to myeloid neoplasms and rarely to lymphoid malignancies. MPLPF inheritance is autosomal dominant. {ECO:0000269|PubMed:25920683, ECO:0000269|PubMed:26712909}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:25920683}.; ",{"$nulls":4},"p.Glu3Gln","c.7G>C","MODERATE","3/640",1,{"$nulls":5},"5","74","75","51","52","69","71","0","0","0","0.1408",{"$nulls":20},"0.416756","1.63",null,"0.999993","0.06",{"$nulls":6},"ExAC_NFE_AF",1.081E-4,{"$nulls":6},"C4225174","0/0","69,0","0","69","0/1","63,11","0.1486","74",null,"chr5:177516910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1538"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DENND3","chr8:141189084","DENND3(Q1061H)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide exchange factor (GEF) activating RAB12. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB12 into its active GTP-bound form (PubMed:20937701). Regulates autophagy in response to starvation through RAB12 activation. Starvation leads to ULK1/2-dependent phosphorylation of Ser-472 and Ser-490, which in turn allows recruitment of 14-3-3 adapter proteins and leads to up-regulation of GEF activity towards RAB12 (By similarity). Also plays a role in protein transport from recycling endosomes to lysosomes, regulating, for instance, the degradation of the transferrin receptor and of the amino acid transporter PAT4 (PubMed:20937701). Starvation also induces phosphorylation at Tyr-858, which leads to up-regulated GEF activity and initiates autophagy (By similarity). {ECO:0000250|UniProtKB:A2RT67, ECO:0000269|PubMed:20937701}.; ",{"$nulls":4},"p.Gln1061His","c.3183G>T","MODERATE","1061/1278",19,{"$nulls":5},"5","569","1211","389","779","523","1078","0","0","0","0.4351",{"$nulls":20},"3.136392","1.55;1.55;1.55;0.22","2.62;.;.;.","0.997706;0.997706;0.998617;0.997706","-3.31;-3.32;-3.46;-3.88","1.0;1.0;.;.","0.001;0.001;0.003;0.0","0.624;0.603;0.699;0.698",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","547,0","0","547","0/1","633,532","0.4567","1165",null,"chr8:141189084:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.4223"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DENND3","chr8:141189084","DENND3(Q1061H)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide exchange factor (GEF) activating RAB12. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB12 into its active GTP-bound form (PubMed:20937701). Regulates autophagy in response to starvation through RAB12 activation. Starvation leads to ULK1/2-dependent phosphorylation of Ser-472 and Ser-490, which in turn allows recruitment of 14-3-3 adapter proteins and leads to up-regulation of GEF activity towards RAB12 (By similarity). Also plays a role in protein transport from recycling endosomes to lysosomes, regulating, for instance, the degradation of the transferrin receptor and of the amino acid transporter PAT4 (PubMed:20937701). Starvation also induces phosphorylation at Tyr-858, which leads to up-regulated GEF activity and initiates autophagy (By similarity). {ECO:0000250|UniProtKB:A2RT67, ECO:0000269|PubMed:20937701}.; ",{"$nulls":4},"p.Gln1061His","c.3183G>T","MODERATE","1061/1278",19,{"$nulls":5},"5","569","1039","389","712","524","946","0","0","0","0.2368",{"$nulls":20},"3.136392","1.55;1.55;1.55;0.22","2.62;.;.;.","0.997706;0.997706;0.998617;0.997706","-3.31;-3.32;-3.46;-3.88","1.0;1.0;.;.","0.001;0.001;0.003;0.0","0.624;0.603;0.699;0.698",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","547,0","0","547","0/1","767,245","0.2421","1012",null,"chr8:141189084:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2374"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DERL1","chr8:123024988","DERL1(V110L)",null,null,"transmembrane region (Helical; Name=3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functional component of endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by forming a channel that allows the retrotranslocation of misfolded proteins into the cytosol where they are ubiquitinated and degraded by the proteasome. May mediate the interaction between VCP and the misfolded protein (PubMed:15215856). Also involved in endoplasmic reticulum stress-induced pre-emptive quality control, a mechanism that selectively attenuates the translocation of newly synthesized proteins into the endoplasmic reticulum and reroutes them to the cytosol for proteasomal degradation (PubMed:26565908). By controlling the steady-state expression of the IGF1R receptor, indirectly regulates the insulin-like growth factor receptor signaling pathway (PubMed:26692333). {ECO:0000269|PubMed:15215856, ECO:0000269|PubMed:26565908, ECO:0000269|PubMed:26692333}.; ",{"$nulls":4},"p.Val110Leu","c.328G>C","MODERATE","110/251",3,{"$nulls":5},"5","178","295","124","201","143","252","0","0","0","0.0595",{"$nulls":20},"3.25182","2.82;1.6;1.62;1.62","1.105;1.105;.;.","1","-1.95;-1.95;-1.82;-1.82","0.007;0.003;.;.","0.171;0.173;0.154;0.154","0.845;0.81;0.852;0.852",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the derlin family. Members of this family participate in the ER-associated degradation response and retrotranslocate misfolded or unfolded proteins from the ER lumen to the cytosol for proteasomal degradation. This protein recognizes substrate in the ER and works in a complex to retrotranslocate it across the ER membrane into the cytosol. This protein may select cystic fibrosis transmembrane conductance regulator protein (CFTR) for degradation as well as unfolded proteins in Alzheimer's disease. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Aug 2012].",null,null,"0/0","169,0","0","169","0/1","261,19","0.0679","280",null,"chr8:123024988:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0697"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DIAPH1","chr5:141527697","DIAPH1(Splicing Acceptor/Donor Loss)",{"$nulls":6},49,"PASS","Splice-site Loss",null,-1,"DISEASE: Deafness, autosomal dominant, 1 (DFNA1) [MIM:124900]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. Patients may have mild thrombocytopenia and enlarged platelets, although most of DFNA1 affected individuals do not have significant bleeding tendencies. {ECO:0000269|PubMed:22938506, ECO:0000269|PubMed:26912466, ECO:0000269|PubMed:27808407, ECO:0000269|PubMed:9360932}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Seizures, cortical blindness, and microcephaly syndrome (SCBMS) [MIM:616632]: A severe autosomal recessive neurodevelopmental disorder characterized by microcephaly, early- onset seizures, severely delayed psychomotor development, short stature, and cortical blindness. {ECO:0000269|PubMed:24781755, ECO:0000269|PubMed:26463574}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Actin nucleation and elongation factor required for the assembly of F-actin structures, such as actin cables and stress fibers (By similarity). Binds to the barbed end of the actin filament and slows down actin polymerization and depolymerization (By similarity). Required for cytokinesis, and transcriptional activation of the serum response factor (By similarity). DFR proteins couple Rho and Src tyrosine kinase during signaling and the regulation of actin dynamics (By similarity). Functions as a scaffold protein for MAPRE1 and APC to stabilize microtubules and promote cell migration (By similarity). Has neurite outgrowth promoting activity. Acts in a Rho-dependent manner to recruit PFY1 to the membrane (By similarity). In hear cells, it may play a role in the regulation of actin polymerization in hair cells (PubMed:20937854, PubMed:21834987, PubMed:26912466). The MEMO1- RHOA-DIAPH1 signaling pathway plays an important role in ERBB2- dependent stabilization of microtubules at the cell cortex (PubMed:20937854, PubMed:21834987). It controls the localization of APC and CLASP2 to the cell membrane, via the regulation of GSK3B activity (PubMed:20937854, PubMed:21834987). In turn, membrane-bound APC allows the localization of the MACF1 to the cell membrane, which is required for microtubule capture and stabilization (PubMed:20937854, PubMed:21834987). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape (PubMed:20937854, PubMed:21834987). Plays a role in brain development (PubMed:24781755). Also acts as an actin nucleation and elongation factor in the nucleus by promoting nuclear actin polymerization inside the nucleus to drive serum-dependent SRF-MRTFA activity (By similarity). {ECO:0000250|UniProtKB:O08808, ECO:0000269|PubMed:20937854, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24781755, ECO:0000269|PubMed:26912466}.; ","gedi",{"$nulls":4},"c.3149-1delG","HIGH",null,23,{"$nulls":5},"1",{"$nulls":15},"(DIAPH1|ENSG00000131504|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Deafness, autosomal dominant 1","Audiologic/Otolaryngologic",{"$nulls":3},"C1852282| C4225261","0/0","54,0","0","69","0/1","36,3","0.0682","44",null,"chr5:141527697:AC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0682"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DIDO1","chr20:62909720","DIDO1(K380N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative transcription factor, weakly pro-apoptotic when overexpressed (By similarity). Tumor suppressor. Required for early embryonic stem cell development. {ECO:0000250, ECO:0000269|PubMed:16127461}.; ",{"$nulls":4},"p.Lys380Asn","c.1140G>T","MODERATE","380/2240",4,{"$nulls":5},"5","352","427","283","347","281","349","0","0","0","0.1318",{"$nulls":20},"2.797141","2.81;2.81;2.45;1.95;1.95;1.95;1.96","2.85","0.9994","-3.01;-3.01;-4.13;-3.92;-3.92;-3.92;-3.92","0.999;0.999;1.0;0.998;0.998;0.998;0.999","0.003;0.003;0.013;0.001;0.001;0.001;0.003","0.578;0.599;0.587;0.593;0.649;0.609;0.586",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","341,0","0","341","0/1","362,51","0.1235","413",null,"chr20:62909720:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.121"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DIO1","chr1:53894252","DIO1(W14C)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Responsible for the deiodination of T4 (3,5,3',5'- tetraiodothyronine) into T3 (3,5,3'-triiodothyronine) and of T3 into T2 (3,3'-diiodothyronine). Plays a role in providing a source of plasma T3 by deiodination of T4 in peripheral tissues such as liver and kidney.; ",{"$nulls":4},"p.Trp14Cys","c.42G>C","MODERATE","14/249",1,{"$nulls":5},"5","254","192","213","163","204","154","0","0","0","0.1169",{"$nulls":20},"3.238365","1.55;1.55;.;.;.;1.55;.;1.55","1.01;1.01;.;.;.;1.01;1.01;1.01","0.999841;0.999841;0.999841;0.999841;0.999841;1","-1.45;-1.54;.;.;.;-3.58;-1.79;-1.27","0.994;0.995;.;.;.;.;0.992;0.982","0.152;0.153;.;.;.;0.156;0.025;0.086","0.256;0.343;0.41;0.422;0.5;0.404;0.403;0.401",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","254,0","0","254","0/1","169,21","0.1105","190",null,"chr1:53894252:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1104"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DNAH8","chr6:39008905","DNAH8(A4436S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Involved in sperm motility; implicated in sperm flagellar assembly (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala4436Ser","c.13306G>T","MODERATE","4436/4707",89,{"$nulls":5},"5","351","369","259","282","282","301","0.0028","0.0028","0","0.1462",{"$nulls":20},"1.976368",".;3.15",".;-0.07","0.970428",".;-0.2",".;0.005",".;0.922","0.156;0.144",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","323,1","0.0031","324","0/1","295,60","0.169","355",null,"chr6:39008905:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1596"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DNAH8","chr6:39008905","DNAH8(A4436S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Involved in sperm motility; implicated in sperm flagellar assembly (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala4436Ser","c.13306G>T","MODERATE","4436/4707",89,{"$nulls":5},"5","351","396","259","293","282","331","0.0028","0.0028","0","0.0725",{"$nulls":20},"1.976368",".;3.15",".;-0.07","0.970428",".;-0.2",".;0.005",".;0.922","0.156;0.144",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","323,1","0.0031","324","0/1","358,27","0.0701","385",null,"chr6:39008905:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0614"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DRD4","chr11:640004","DRD4(R252P)",{"$nulls":6},62,"PASS","Missense",null,-1,null,"FUNCTION: Dopamine receptor responsible for neuronal signaling in the mesolimbic system of the brain, an area of the brain that regulates emotion and complex behavior. Activated by dopamine, but also by epinephrine and norepinephrine, and by numerous synthetic agonists and drugs (PubMed:9003072, PubMed:16423344, PubMed:27659709, PubMed:29051383). Agonist binding triggers signaling via G proteins that inhibit adenylyl cyclase (PubMed:7512953, PubMed:7643093, PubMed:16423344, PubMed:27659709, PubMed:29051383). Modulates the circadian rhythm of contrast sensitivity by regulating the rhythmic expression of NPAS2 in the retinal ganglion cells (By similarity). {ECO:0000250|UniProtKB:P51436, ECO:0000269|PubMed:16423344, ECO:0000269|PubMed:1840645, ECO:0000269|PubMed:27659709, ECO:0000269|PubMed:29051383, ECO:0000269|PubMed:7512953, ECO:0000269|PubMed:7643093, ECO:0000269|PubMed:8078498, ECO:0000269|PubMed:9003072}.; ",{"$nulls":4},"p.Arg252Pro","c.755G>C","MODERATE","252/419",3,{"$nulls":5},"1",{"$nulls":30},"0.592493","-0.3",null,"1","-0.86",null,"0.245","0.114",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes the D4 subtype of the dopamine receptor. The D4 subtype is a G-protein coupled receptor which inhibits adenylyl cyclase. It is a target for drugs which treat schizophrenia and Parkinson disease. Mutations in this gene have been associated with various behavioral phenotypes, including autonomic nervous system dysfunction, attention deficit/hyperactivity disorder, and the personality trait of novelty seeking. This gene contains a polymorphic number (2-10 copies) of tandem 48 nt repeats; the sequence shown contains four repeats. [provided by RefSeq, Jul 2008].  ",null,"C1263846","0/0","114,0","0","115","0/1","65,6","0.0845","71",null,"chr11:640004:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0845"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DST","chr6:56609341","DST(D1552N)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 6. ), splice variant (In isoform 7. ), splice variant (In isoform 8. ), splice variant (In isoform 3. ), splice variant (In isoform 2. ), splice variant (In isoform 9. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neuropathy, hereditary sensory and autonomic, 6 (HSAN6) [MIM:614653]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN6 is a severe autosomal recessive disorder characterized by neonatal hypotonia, respiratory and feeding difficulties, lack of psychomotor development, and autonomic abnormalities including labile cardiovascular function, lack of corneal reflexes leading to corneal scarring, areflexia, and absent axonal flare response after intradermal histamine injection. {ECO:0000269|PubMed:22522446}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa simplex, autosomal recessive 2 (EBSB2) [MIM:615425]: A form of epidermolysis bullosa, a dermatologic disorder characterized by localized blistering on the dorsal, lateral and plantar surfaces of the feet. EBSB2 is characterized by trauma-induced blistering mainly occurring on the feet and ankles. Ultrastructural analysis of skin biopsy shows abnormal hemidesmosomes with poorly formed inner plaques. {ECO:0000269|PubMed:20164846, ECO:0000269|PubMed:22113475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cytoskeletal linker protein. Acts as an integrator of intermediate filaments, actin and microtubule cytoskeleton networks. Required for anchoring either intermediate filaments to the actin cytoskeleton in neural and muscle cells or keratin- containing intermediate filaments to hemidesmosomes in epithelial cells. The proteins may self-aggregate to form filaments or a two- dimensional mesh. Regulates the organization and stability of the microtubule network of sensory neurons to allow axonal transport. Mediates docking of the dynein/dynactin motor complex to vesicle cargos for retrograde axonal transport through its interaction with TMEM108 and DCTN1 (By similarity). {ECO:0000250|UniProtKB:Q91ZU6}.; FUNCTION: Isoform 6: required for bundling actin filaments around the nucleus. {ECO:0000250, ECO:0000269|PubMed:10428034, ECO:0000269|PubMed:12482924, ECO:0000269|PubMed:19403692}.; ",{"$nulls":4},"p.Asp1552Asn","c.4654G>A","MODERATE","1552/7461",36,{"$nulls":5},"5","126","135","102","103","118","129","0","0","0","0.0853",{"$nulls":20},"1.671775","-0.29",null,null,"-0.56;-0.8",".;0.066","0.143;0.142","0.157;.",{"$nulls":3},"Unknown",-1,"AR","Neuropathy, hereditary sensory and autonomic, type VI","Neurologic",null,"This gene encodes a member of the plakin protein family of adhesion junction plaque proteins. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene, but the full-length nature of some variants has not been defined. It has been reported that some isoforms are expressed in neural and muscle tissue, anchoring neural intermediate filaments to the actin cytoskeleton, and some isoforms are expressed in epithelial tissue, anchoring keratin-containing intermediate filaments to hemidesmosomes. Consistent with the expression, mice defective for this gene show skin blistering and neurodegeneration. [provided by RefSeq, Mar 2010].",null,"C3809470| C3539003","0/0","129,0","0","129","0/1","120,12","0.0909","132",null,"chr6:56609341:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0971"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DTNA","chr18:34875321","DTNA(A582G)",null,null,"splice variant (In isoform 7 and isoform 9. ), splice variant (In isoform 3, isoform 4, isoform 5, isoform 8, isoform 12 and isoform 16. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Left ventricular non-compaction 1 (LVNC1) [MIM:604169]: A form of left ventricular non-compaction, a cardiomyopathy due to myocardial morphogenesis arrest and characterized by a hypertrophic left ventricle, a severely thickened 2-layered myocardium, numerous prominent trabeculations, deep intertrabecular recesses, and poor systolic function. Clinical manifestations are variable. Some affected individuals experience no symptoms at all, others develop heart failure. In some cases, left ventricular non-compaction is associated with other congenital heart anomalies. LVNC1 is an autosomal dominant condition. {ECO:0000269|PubMed:11238270}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be involved in the formation and stability of synapses as well as being involved in the clustering of nicotinic acetylcholine receptors.; ",{"$nulls":4},"p.Ala582Gly","c.1745C>G","MODERATE","582/743",17,{"$nulls":5},"5","649","851","458","616","526","723","0","0","0","0.1217",{"$nulls":20},"1.8172139999999999","2.08;2.06;2.05;2.08;2.08;2.05;2.05;.;.;.;.;.",".;.;.;.;.;1.27;1.27;.;.;.;.;.","0.968934;0.989476;0.989476;0.991898;0.991898;0.968934;0.97577;0.989476;0.991898","-1.86;.;.;.;.;-1.92;-1.92;.;-1.8;.;-1.92;.","0.002;.;.;.;0.002;0.001;0.001;.;.;0.127;.;.","0.085;.;.;.;.;0.095;0.095;.;0.068;.;0.058;.","0.239;0.244;0.231;0.241;0.232;0.191;0.177;0.25;0.274;0.257;0.246;0.267",{"$nulls":3},"Unknown",-1,"AD","Left ventricular noncompaction 1","Cardiovascular",{"$nulls":3},"C1858725","0/0","614,0","0","614","0/1","699,90","0.1141","789",null,"chr18:34875321:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1104"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","DYNC1LI1","chr3:32526801","DYNC1LI1(Ter524Rext*?)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. May play a role in binding dynein to membranous organelles or chromosomes. Probably involved in the microtubule-dependent transport of pericentrin. Is required for progress through the spindle assembly checkpoint. The phosphorylated form appears to be involved in the selective removal of MAD1L1 and MAD1L2 but not BUB1B from kinetochores. {ECO:0000269|PubMed:19229290}.; ",{"$nulls":4},"p.Ter524Argext*?","c.1570T>C","HIGH","524/523",13,{"$nulls":5},"5","453","419","357","333","349","333","0","0","0","0.2162",{"$nulls":20},"1.909725",null,null,"1",{"$nulls":3},"0.161;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","435,0","0","435","0/1","321,86","0.2113","407",null,"chr3:32526801:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2192"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","DYNC1LI1","chr3:32526801","DYNC1LI1(Ter524Rext*?)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. May play a role in binding dynein to membranous organelles or chromosomes. Probably involved in the microtubule-dependent transport of pericentrin. Is required for progress through the spindle assembly checkpoint. The phosphorylated form appears to be involved in the selective removal of MAD1L1 and MAD1L2 but not BUB1B from kinetochores. {ECO:0000269|PubMed:19229290}.; ",{"$nulls":4},"p.Ter524Argext*?","c.1570T>C","HIGH","524/523",13,{"$nulls":5},"5","453","471","357","377","346","379","0","0","0","0.095",{"$nulls":20},"1.909725",null,null,"1",{"$nulls":3},"0.161;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","436,0","0","436","0/1","423,39","0.0844","462",null,"chr3:32526801:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0875"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","E4F1","chr16:2232790","E4F1(K255N)",null,null,"zinc finger region (C2H2-type 3; degenerate ), region of interest (Mediates dimerization, DNA-binding, transcription repression of CCNA2 and interaction with HMGA2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as a transcriptional repressor. May also function as a ubiquitin ligase mediating ubiquitination of chromatin-associated TP53. Functions in cell survival and proliferation through control of the cell cycle. Functions in the p53 and pRB tumor suppressor pathways and regulates the cyclin CCNA2 transcription.; ",{"$nulls":4},"p.Lys255Asn","c.765G>C","MODERATE","255/784",6,{"$nulls":5},"5","398","391","298","288","317","326","0","0","0","0.138",{"$nulls":20},"3.6325760000000002","1.28","2.895;.;.;.","0.993739;0.92561;0.993739","-3.91;-3.61;-4.02;-3.79","0.979;.;.;.","0.004;0.015;0.007;0.031","0.675;0.609;0.62;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","380,0","0","380","0/1","318,48","0.1311","366",null,"chr16:2232790:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1319"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","E4F1","chr16:2232790","E4F1(K255N)",null,null,"zinc finger region (C2H2-type 3; degenerate ), region of interest (Mediates dimerization, DNA-binding, transcription repression of CCNA2 and interaction with HMGA2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as a transcriptional repressor. May also function as a ubiquitin ligase mediating ubiquitination of chromatin-associated TP53. Functions in cell survival and proliferation through control of the cell cycle. Functions in the p53 and pRB tumor suppressor pathways and regulates the cyclin CCNA2 transcription.; ",{"$nulls":4},"p.Lys255Asn","c.765G>C","MODERATE","255/784",6,{"$nulls":5},"5","398","429","298","331","317","362","0","0","0","0.0856",{"$nulls":20},"3.6325760000000002","1.28","2.895;.;.;.","0.993739;0.92561;0.993739","-3.91;-3.61;-4.02;-3.79","0.979;.;.;.","0.004;0.015;0.007;0.031","0.675;0.609;0.62;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","385,0","0","385","0/1","383,34","0.0815","417",null,"chr16:2232790:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0846"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ECE2","chr3:184290316","ECE2(K656R)",null,null,"topological domain (Lumenal ), domain (Peptidase M13 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs1482075807",-1,null,"FUNCTION: Converts big endothelin-1 to endothelin-1. Also involved in the processing of various neuroendocrine peptides, including neurotensin, angiotensin I, substance P, proenkephalin-derived peptides, and prodynorphin-derived peptides. May play a role in amyloid-beta processing (By similarity). {ECO:0000250|UniProtKB:B2RQR8, ECO:0000269|PubMed:12560336}.; ",{"$nulls":4},"p.Lys656Arg","c.1967A>G","MODERATE","656/883",14,{"$nulls":5},"5","355","308","239","208","331","271","0","0","0","0.1993",{"$nulls":20},"2.656103","-1.52",null,"1;0.995784;0.995784;0.995784;0.995784","0.11;0.11;0.11;0.11;0.1",null,"0.714;0.98;0.955;0.86;0.849","0.112;0.115;0.116;0.116;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","347,0","0","347","0/1","231,64","0.2169","295",null,"chr3:184290316:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2115"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ECE2","chr3:184290316","ECE2(K656R)",null,null,"topological domain (Lumenal ), domain (Peptidase M13 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs1482075807",-1,null,"FUNCTION: Converts big endothelin-1 to endothelin-1. Also involved in the processing of various neuroendocrine peptides, including neurotensin, angiotensin I, substance P, proenkephalin-derived peptides, and prodynorphin-derived peptides. May play a role in amyloid-beta processing (By similarity). {ECO:0000250|UniProtKB:B2RQR8, ECO:0000269|PubMed:12560336}.; ",{"$nulls":4},"p.Lys656Arg","c.1967A>G","MODERATE","656/883",14,{"$nulls":5},"5","355","438","239","307","329","386","0","0","0","0.1036",{"$nulls":20},"2.656103","-1.52",null,"1;0.995784;0.995784;0.995784;0.995784","0.11;0.11;0.11;0.11;0.1",null,"0.714;0.98;0.955;0.86;0.849","0.112;0.115;0.116;0.116;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","339,0","0","339","0/1","375,45","0.1071","420",null,"chr3:184290316:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1173"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","EDN2","chr1:41482542","EDN2(R90G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Endothelins are endothelium-derived vasoconstrictor peptides.; ",{"$nulls":4},"p.Arg90Gly","c.268C>G","MODERATE","90/178",3,{"$nulls":5},"5","444","540","280","366","392","489","0","0","0","0.0838",{"$nulls":20},"4.096186","-1.97","3.015","0.988488","-2.9","1.0","0.025","0.546",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","424,0","0","424","0/1","473,46","0.0886","519",null,"chr1:41482542:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0874"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","EGF","chr4:109961942","EGF(C423*)",{"$nulls":3},"disulfide-bond:experimental_evidence_used_in_manual_assertion","MODERATE",null,255,"PASS","Loss Of Function",null,-1,"DISEASE: Hypomagnesemia 4 (HOMG4) [MIM:611718]: A disorder characterized by massive renal hypomagnesemia and normal levels of serum calcium and calcium excretion. Clinical features include seizures, mild-to moderate psychomotor retardation, and brisk tendon reflexes. {ECO:0000269|PubMed:17671655}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: EGF stimulates the growth of various epidermal and epithelial tissues in vivo and in vitro and of some fibroblasts in cell culture. Magnesiotropic hormone that stimulates magnesium reabsorption in the renal distal convoluted tubule via engagement of EGFR and activation of the magnesium channel TRPM6. Can induce neurite outgrowth in motoneurons of the pond snail Lymnaea stagnalis in vitro (PubMed:10964941). {ECO:0000269|PubMed:10964941, ECO:0000269|PubMed:17671655}.; ","level2",{"$nulls":3},"p.Cys423*","c.1269T>A","HIGH","423/1207",8,{"$nulls":5},"4","834","871","538","575","756","778","0","0","0","0.2699",{"$nulls":5},"(EGF|ENSG00000138798|1|1.00)","(EGF|ENSG00000138798|1|1.00)",{"$nulls":13},"7.167371",null,null,"1",{"$nulls":3},"0.915;0.968;0.912",{"$nulls":3},"Unknown",-1,"AR","Hypomagnesemia 4, renal","Renal","kCANCER,kERBB,kMAPK",null,null,"C2673648","0/0","761,0","0","761","0/1","591,224","0.2748","815",null,"chr4:109961942:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2765"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","EGF","chr4:109961942","EGF(C423*)",{"$nulls":3},"disulfide-bond:experimental_evidence_used_in_manual_assertion","MODERATE",null,255,"PASS","Loss Of Function",null,-1,"DISEASE: Hypomagnesemia 4 (HOMG4) [MIM:611718]: A disorder characterized by massive renal hypomagnesemia and normal levels of serum calcium and calcium excretion. Clinical features include seizures, mild-to moderate psychomotor retardation, and brisk tendon reflexes. {ECO:0000269|PubMed:17671655}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: EGF stimulates the growth of various epidermal and epithelial tissues in vivo and in vitro and of some fibroblasts in cell culture. Magnesiotropic hormone that stimulates magnesium reabsorption in the renal distal convoluted tubule via engagement of EGFR and activation of the magnesium channel TRPM6. Can induce neurite outgrowth in motoneurons of the pond snail Lymnaea stagnalis in vitro (PubMed:10964941). {ECO:0000269|PubMed:10964941, ECO:0000269|PubMed:17671655}.; ","level2",{"$nulls":3},"p.Cys423*","c.1269T>A","HIGH","423/1207",8,{"$nulls":5},"4","834","961","538","628","756","861","0","0","0","0.1289",{"$nulls":5},"(EGF|ENSG00000138798|1|1.00)","(EGF|ENSG00000138798|1|1.00)",{"$nulls":13},"7.167371",null,null,"1",{"$nulls":3},"0.915;0.968;0.912",{"$nulls":3},"Unknown",-1,"AR","Hypomagnesemia 4, renal","Renal","kCANCER,kERBB,kMAPK",null,null,"C2673648","0/0","766,0","0","766","0/1","783,119","0.1319","902",null,"chr4:109961942:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1354"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","EIF3F","chr11:7994984","EIF3F(D250H)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre- initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF- 3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). {ECO:0000255|HAMAP-Rule:MF_03005, ECO:0000269|PubMed:17581632, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.; ",{"$nulls":4},"p.Asp250His","c.748G>C","MODERATE","250/357",6,{"$nulls":5},"5","348","334","290","284","302","273","0","0","0","0.1758",{"$nulls":20},"4.244697","1.27","2.67","1","-3.39","0.995","0.002","0.961",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4749019","0/0","344,0","0","344","0/1","278,54","0.1627","332",null,"chr11:7994984:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1655"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","EIF3F","chr11:7994984","EIF3F(D250H)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre- initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF- 3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). {ECO:0000255|HAMAP-Rule:MF_03005, ECO:0000269|PubMed:17581632, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.; ",{"$nulls":4},"p.Asp250His","c.748G>C","MODERATE","250/357",6,{"$nulls":5},"5","348","394","290","323","303","339","0","0","0","0.0796",{"$nulls":20},"4.244697","1.27","2.67","1","-3.39","0.995","0.002","0.961",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4749019","0/0","344,0","0","344","0/1","359,31","0.0795","390",null,"chr11:7994984:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0805"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ELMOD2","chr4:140537534","ELMOD2(L131R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a GTPase-activating protein (GAP) toward guanine nucleotide exchange factors like ARL2, ARL3, ARF1 and ARF6, but not for GTPases outside the Arf family. Regulates IFN-related antiviral responses. {ECO:0000269|PubMed:17452337, ECO:0000269|PubMed:19966137}.; ",{"$nulls":4},"p.Leu131Arg","c.392T>G","MODERATE","131/293",5,{"$nulls":5},"4","186","223","110","138",null,null,"0","0",{"$nulls":22},"4.137862","0.22","3.5;.;.","1","-5.84;-5.99;-5.87","1.0;.;.","0.0","0.99;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","178,0","0","178","0/1","206,12","0.055","218",null,"chr4:140537534:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0507"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","EML6","chr2:54827664","EML6(E208D)",null,null,"repeat (WD 4 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. {ECO:0000250}.; ",{"$nulls":4},"p.Glu208Asp","c.624A>C","MODERATE","208/1958",5,{"$nulls":5},"5","490","642","371","484","412","550","0","0","0","0.1164",{"$nulls":20},"0.799649","3.63","-0.68","0.546929","1.04",null,"1.0","0.146",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","471,0","0","471","0/1","548,69","0.1118","617",null,"chr2:54827664:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1178"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ENAH","chr1:225519204","ENAH(S270R)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Ena/VASP proteins are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance and lamellipodial and filopodial dynamics in migrating cells. ENAH induces the formation of F-actin rich outgrowths in fibroblasts. Acts synergistically with BAIAP2-alpha and downstream of NTN1 to promote filipodia formation (By similarity). {ECO:0000250, ECO:0000269|PubMed:11696321, ECO:0000269|PubMed:18158903}.; ",{"$nulls":4},"p.Ser270Arg","c.808A>C","MODERATE","270/802",6,{"$nulls":5},"5","451","473","324","343","301","338","0","0","0","0.1361",{"$nulls":20},"1.479373","-2.72;.;-2.72","1.15;.;1.15","1","-1.38;.;-1.38","0.006;.;0.01","0.024;.;0.11","0.245;0.208;0.278",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","419,0","0","419","0/1","379,58","0.1327","437",null,"chr1:225519204:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1079"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ENPP1","chr6:131808147","ENPP1(E38Q)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs1275709620",-1,"DISEASE: Ossification of the posterior longitudinal ligament of the spine (OPLL) [MIM:602475]: A calcification of the posterior longitudinal ligament of the spinal column, usually at the level of the cervical spine. Patients with OPLL frequently present with a severe myelopathy that can lead to tetraparesis. {ECO:0000269|PubMed:10453738}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Arterial calcification of infancy, generalized, 1 (GACI1) [MIM:208000]: A severe autosomal recessive disorder characterized by calcification of the internal elastic lamina of muscular arteries and stenosis due to myointimal proliferation. The disorder is often fatal within the first 6 months of life because of myocardial ischemia resulting in refractory heart failure. {ECO:0000269|PubMed:12881724, ECO:0000269|PubMed:15605415, ECO:0000269|PubMed:15940697, ECO:0000269|PubMed:20016754, ECO:0000269|PubMed:22209248, ECO:0000269|PubMed:23430823, ECO:0000269|PubMed:27467858}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:16186408}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hypophosphatemic rickets, autosomal recessive, 2 (ARHR2) [MIM:613312]: A hereditary form of hypophosphatemic rickets, a disorder of proximal renal tubule function that causes phosphate loss, hypophosphatemia and skeletal deformities, including rickets and osteomalacia unresponsive to vitamin D. Symptoms are bone pain, fractures and growth abnormalities. {ECO:0000269|PubMed:20137772, ECO:0000269|PubMed:20137773, ECO:0000269|PubMed:25741938}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cole disease (COLED) [MIM:615522]: A rare autosomal dominant genodermatosis characterized by punctate keratoderma associated with irregularly shaped hypopigmented macules, which are typically found over the arms and legs but not the trunk or acral regions. Skin biopsies of palmoplantar lesions show hyperorthokeratosis, hypergranulosis, and acanthosis. Hypopigmented areas of skin, however, reveal a reduction in melanin content in keratinocytes but not in melanocytes, as well as hyperkeratosis and a normal number of melanocytes. Ultrastructurally, melanocytes show a disproportionately large number of melanosomes in the cytoplasm and dendrites, whereas keratinocytes show a paucity of these organelles, suggestive of impaired melanosome transfer. Some patients also exhibit calcinosis cutis or calcific tendinopathy. {ECO:0000269|PubMed:24075184, ECO:0000269|PubMed:26617416}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: By generating PPi, plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. PPi inhibits mineralization by binding to nascent hydroxyapatite (HA) crystals, thereby preventing further growth of these crystals. Preferentially hydrolyzes ATP, but can also hydrolyze other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity and function. {ECO:0000269|PubMed:10615944, ECO:0000269|PubMed:27467858, ECO:0000269|PubMed:8001561}.; ",{"$nulls":4},"p.Glu38Gln","c.112G>C","MODERATE","38/925",1,{"$nulls":5},"5","45","35","37","28","29","25","0","0","0","0.28",{"$nulls":20},"1.144011","-0.76;.","0.55","1","0.01;.","0.199","0.143;.","0.066;.",{"$nulls":3},"Unknown",-1,"AR","Hypophosphatemic rickets, autosomal recessive 2; Arterial calcification, generalized, of infancy, 1","Cardiovascular; Dermatologic; Musculoskeletal; Renal",{"$nulls":3},"C0028754| C2750078| C3809781| C0011860| C4551985","0/0","42,0","0","42","0/1","25,9","0.2647","34",null,"chr6:131808147:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2143"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ENPP1","chr6:131808147","ENPP1(E38Q)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs1275709620",-1,"DISEASE: Ossification of the posterior longitudinal ligament of the spine (OPLL) [MIM:602475]: A calcification of the posterior longitudinal ligament of the spinal column, usually at the level of the cervical spine. Patients with OPLL frequently present with a severe myelopathy that can lead to tetraparesis. {ECO:0000269|PubMed:10453738}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Arterial calcification of infancy, generalized, 1 (GACI1) [MIM:208000]: A severe autosomal recessive disorder characterized by calcification of the internal elastic lamina of muscular arteries and stenosis due to myointimal proliferation. The disorder is often fatal within the first 6 months of life because of myocardial ischemia resulting in refractory heart failure. {ECO:0000269|PubMed:12881724, ECO:0000269|PubMed:15605415, ECO:0000269|PubMed:15940697, ECO:0000269|PubMed:20016754, ECO:0000269|PubMed:22209248, ECO:0000269|PubMed:23430823, ECO:0000269|PubMed:27467858}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:16186408}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hypophosphatemic rickets, autosomal recessive, 2 (ARHR2) [MIM:613312]: A hereditary form of hypophosphatemic rickets, a disorder of proximal renal tubule function that causes phosphate loss, hypophosphatemia and skeletal deformities, including rickets and osteomalacia unresponsive to vitamin D. Symptoms are bone pain, fractures and growth abnormalities. {ECO:0000269|PubMed:20137772, ECO:0000269|PubMed:20137773, ECO:0000269|PubMed:25741938}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cole disease (COLED) [MIM:615522]: A rare autosomal dominant genodermatosis characterized by punctate keratoderma associated with irregularly shaped hypopigmented macules, which are typically found over the arms and legs but not the trunk or acral regions. Skin biopsies of palmoplantar lesions show hyperorthokeratosis, hypergranulosis, and acanthosis. Hypopigmented areas of skin, however, reveal a reduction in melanin content in keratinocytes but not in melanocytes, as well as hyperkeratosis and a normal number of melanocytes. Ultrastructurally, melanocytes show a disproportionately large number of melanosomes in the cytoplasm and dendrites, whereas keratinocytes show a paucity of these organelles, suggestive of impaired melanosome transfer. Some patients also exhibit calcinosis cutis or calcific tendinopathy. {ECO:0000269|PubMed:24075184, ECO:0000269|PubMed:26617416}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: By generating PPi, plays a role in regulating pyrophosphate levels, and functions in bone mineralization and soft tissue calcification. PPi inhibits mineralization by binding to nascent hydroxyapatite (HA) crystals, thereby preventing further growth of these crystals. Preferentially hydrolyzes ATP, but can also hydrolyze other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates with release of pyrophosphate and diadenosine polyphosphates, and also 3',5'-cAMP to AMP. May also be involved in the regulation of the availability of nucleotide sugars in the endoplasmic reticulum and Golgi, and the regulation of purinergic signaling. Appears to modulate insulin sensitivity and function. {ECO:0000269|PubMed:10615944, ECO:0000269|PubMed:27467858, ECO:0000269|PubMed:8001561}.; ",{"$nulls":4},"p.Glu38Gln","c.112G>C","MODERATE","38/925",1,{"$nulls":5},"4","45","55",null,null,"29","46","0","0","0","0.1087",{"$nulls":20},"1.144011","-0.76;.","0.55","1","0.01;.","0.199","0.143;.","0.066;.",{"$nulls":3},"Unknown",-1,"AR","Hypophosphatemic rickets, autosomal recessive 2; Arterial calcification, generalized, of infancy, 1","Cardiovascular; Dermatologic; Musculoskeletal; Renal",{"$nulls":3},"C0028754| C2750078| C3809781| C0011860| C4551985","0/0","42,0","0","42","0/1","50,5","0.0909","55",null,"chr6:131808147:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ENTPD8","chr9:137438083","ENTPD8(F43Y)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Canalicular ectonucleoside NTPDase responsible for the main hepatic NTPDase activity. Ectonucleoside NTPDases catalyze the hydrolysis of gamma- and beta-phosphate residues of nucleotides, playing a central role in concentration of extracellular nucleotides. Has activity toward ATP, ADP, UTP and UDP, but not toward AMP. {ECO:0000269|PubMed:16752921, ECO:0000269|PubMed:17095758}.; ",{"$nulls":4},"p.Phe43Tyr","c.128T>A","MODERATE","43/495",3,{"$nulls":5},"5","398","422","296","299","347","362","0","0","0","0.1188",{"$nulls":20},"1.8377780000000001","3.21","0.615;0.615;0.615;.","0.946471","1.67;1.77;1.77;1.74","0.201;0.069;0.069;.","1.0","0.284;0.261;0.266;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","393,0","0","393","0/1","352,54","0.133","406",null,"chr9:137438083:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1137"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","EPAS1","chr2:46346888","EPAS1(R14S)",null,null,"domain (bHLH )","domain:bHLH","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Erythrocytosis, familial, 4 (ECYT4) [MIM:611783]: An autosomal dominant disorder characterized by increased serum red blood cell mass, elevated serum hemoglobin and hematocrit, and normal platelet and leukocyte counts. {ECO:0000269|PubMed:18184961, ECO:0000269|PubMed:18378852, ECO:0000269|PubMed:19208626, ECO:0000269|PubMed:22367913}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor involved in the induction of oxygen regulated genes. Heterodimerizes with ARNT; heterodimer binds to core DNA sequence 5'-TACGTG-3' within the hypoxia response element (HRE) of target gene promoters (By similarity). Regulates the vascular endothelial growth factor (VEGF) expression and seems to be implicated in the development of blood vessels and the tubular system of lung. May also play a role in the formation of the endothelium that gives rise to the blood brain barrier. Potent activator of the Tie-2 tyrosine kinase expression. Activation requires recruitment of transcriptional coactivators such as CREBBP and probably EP300. Interaction with redox regulatory protein APEX seems to activate CTAD (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:P97481}.; ","level2",{"$nulls":3},"p.Arg14Ser","c.42G>C","MODERATE","14/870",2,{"$nulls":5},"5","213","265","193","232","153","205","0","0","0","0.1659",{"$nulls":20},"2.795623","2.07",".;2.825","0.999993","-4.4;-4.35",".;0.747","0.006;0.002",".;0.455",{"$nulls":3},"Unknown",-1,"AD","Erthyrocytosis, familial 4","Hematologic; Oncologic","kCANCER",null,null,"C2673187","0/0","209,0","0","209","0/1","220,36","0.1406","256",null,"chr2:46346888:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1422"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","EPAS1","chr2:46346888","EPAS1(R14S)",null,null,"domain (bHLH )","domain:bHLH","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Erythrocytosis, familial, 4 (ECYT4) [MIM:611783]: An autosomal dominant disorder characterized by increased serum red blood cell mass, elevated serum hemoglobin and hematocrit, and normal platelet and leukocyte counts. {ECO:0000269|PubMed:18184961, ECO:0000269|PubMed:18378852, ECO:0000269|PubMed:19208626, ECO:0000269|PubMed:22367913}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor involved in the induction of oxygen regulated genes. Heterodimerizes with ARNT; heterodimer binds to core DNA sequence 5'-TACGTG-3' within the hypoxia response element (HRE) of target gene promoters (By similarity). Regulates the vascular endothelial growth factor (VEGF) expression and seems to be implicated in the development of blood vessels and the tubular system of lung. May also play a role in the formation of the endothelium that gives rise to the blood brain barrier. Potent activator of the Tie-2 tyrosine kinase expression. Activation requires recruitment of transcriptional coactivators such as CREBBP and probably EP300. Interaction with redox regulatory protein APEX seems to activate CTAD (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:P97481}.; ","level2",{"$nulls":3},"p.Arg14Ser","c.42G>C","MODERATE","14/870",2,{"$nulls":5},"4","213","257",null,null,"152","199","0","0","0","0.0905",{"$nulls":20},"2.795623","2.07",".;2.825","0.999993","-4.4;-4.35",".;0.747","0.006;0.002",".;0.455",{"$nulls":3},"Unknown",-1,"AD","Erthyrocytosis, familial 4","Hematologic; Oncologic","kCANCER",null,null,"C2673187","0/0","211,0","0","211","0/1","234,19","0.0751","253",null,"chr2:46346888:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","EXT1","chr8:118110572","EXT1(D159H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Tricho-rhino-phalangeal syndrome 2 (TRPS2) [MIM:150230]: A syndrome that combines the clinical features of tricho-rhino- phalangeal syndrome type 1 and multiple exostoses type 1. Affected individuals manifest multiple dysmorphic facial features including large, laterally protruding ears, a bulbous nose, an elongated upper lip, as well as sparse scalp hair, winged scapulae, multiple cartilaginous exostoses, redundant skin, and mental retardation. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration resulting in the loss of functional copies of TRPS1 and EXT1 has been found in TRPS2 patients.; DISEASE: Chondrosarcoma (CHDSA) [MIM:215300]: A malignant neoplasm derived from cartilage cells. Chondrosarcomas range from slow- growing non-metastasizing lesions to highly aggressive metastasizing sarcomas. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Appears to be a tumor suppressor. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:11518722, ECO:0000269|PubMed:22660413}.; ","gedi|level2",{"$nulls":3},"p.Asp159His","c.475G>C","MODERATE","159/746",1,{"$nulls":5},"4","1699","3960","1292","2968","1483","3470","0","0","0","0.0527",{"$nulls":20},"4.196488","-4.52","3.415","1","-5.4","1.0","0.005","0.911",{"$nulls":3},"Unknown",-1,"AD","Exostoses, multiple, type 1","Musculoskeletal; Oncologic","COSMIC,vGLI",null,null,"C0008479| C0015306","0/0","1380,0","0","1380","0/1","2972,182","0.0577","3154",null,"chr8:118110572:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0536"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FAM107B","chr10:14521961","FAM107B(D238N)",{"$nulls":6},255,"PASS","Missense","rs139987994",4.5392646391284613E-4,{"$nulls":6},"p.Asp238Asn","c.712G>A","MODERATE","238/306",4,{"$nulls":5},"5","139","162","92","103","133","147","0","0","0","0.0748",{"$nulls":20},"3.687164","0.89;.;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89","0.975;0.975;.;0.975;0.975;0.975;0.975;0.975;0.975;0.975;0.975;.;.;.;.;.;.;.;.;.","1","-1.29;.;-1.56;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.29;-1.12;-1.19;-1.19;-1.09;-0.45","0.943;0.943;1.0;0.943;0.943;0.943;0.943;0.943;0.943;0.943;0.943;.;.;.;.;.;.;.;.;.","0.644;.;0.14;0.644;0.644;0.644;0.644;0.644;0.644;0.644;0.644;0.644;0.643;0.665;0.664;0.619;0.841;0.597;0.663;0.809","0.433;0.436;0.411;0.436;0.409;0.436;0.436;0.436;0.436;0.436;0.409;.;.;.;.;.;.;.;.;.",{"$nulls":3},"ESP6500_AA_AF",4.5392646391284613E-4,{"$nulls":7},"0/0","138,0","0","138","0/1","150,11","0.0683","161",null,"chr10:14521961:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0874"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FAM185A","chr7:102749259","FAM185A(R18G)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg18Gly","c.52C>G","MODERATE","18/392",1,1,{"$nulls":4},"4","453","485","307","338","414","156","0","0","0","0.2436",{"$nulls":20},"-0.774597","-1.05","1.1;.;1.1","1","-0.59;-0.72;-0.6","0.0;.;0.0","0.0;0.632;0.479","0.083;.;0.069",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","442,0","0","442","0/1","395,77","0.1631","472",null,"chr7:102749259:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1568"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FAM185A","chr7:102749259","FAM185A(R18G)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg18Gly","c.52C>G","MODERATE","18/392",1,1,{"$nulls":4},"3",null,null,"307","372","413","170",null,null,"0","0.1118",{"$nulls":20},"-0.774597","-1.05","1.1;.;1.1","1","-0.59;-0.72;-0.6","0.0;.;0.0","0.0;0.632;0.479","0.083;.;0.069",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","442,0","0","442","0/1","463,40","0.0795","503",null,"chr7:102749259:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.078"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FAM20B","chr1:179064483","FAM20B(D309H)",null,null,"topological domain (Lumenal ), metal ion-binding site (Manganese), binding site (ATP), disulfide bond ","binding-site:ATP, metal-binding-site:Manganese","LOW, LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG- protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1- O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized. {ECO:0000269|PubMed:19473117, ECO:0000269|PubMed:24425863}.; ",{"$nulls":4},"p.Asp309His","c.925G>C","MODERATE","309/409",6,{"$nulls":5},"5","351","340","245","231","326","300","0","0","0","0.2733",{"$nulls":20},"4.396408","-1.43","3.125","1","-6.82","1.0",null,"0.995",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","346,0","0","346","0/1","240,90","0.2727","330",null,"chr1:179064483:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2857"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FAM20B","chr1:179064483","FAM20B(D309H)",null,null,"topological domain (Lumenal ), metal ion-binding site (Manganese), binding site (ATP), disulfide bond ","binding-site:ATP, metal-binding-site:Manganese","LOW, LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Responsible for the 2-O-phosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature GAG chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG- protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1- O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-phosphorylation may influence the catalytic activity of B3GAT3 (GlcAT-I) which completes the precursor tetrasaccharide of GAG-protein linkage regions on which the repeating disaccharide region is synthesized. {ECO:0000269|PubMed:19473117, ECO:0000269|PubMed:24425863}.; ",{"$nulls":4},"p.Asp309His","c.925G>C","MODERATE","309/409",6,{"$nulls":5},"5","351","417","245","287","324","383","0","0","0","0.1044",{"$nulls":20},"4.396408","-1.43","3.125","1","-6.82","1.0",null,"0.995",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","349,0","0","349","0/1","361,48","0.1174","409",null,"chr1:179064483:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.115"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FAM26E","chr6:116515832","FAM26E(T258K)",{"$nulls":6},255,"PASS","Missense","rs200089126",0.0001512,{"$nulls":6},"p.Thr258Lys","c.773C>A","MODERATE","258/309",2,{"$nulls":5},"4","375","439","287","337","327","384","0","0","0","0.1172",{"$nulls":20},"1.485392","2.37",null,"0.999973;1","-0.16","0.178","0.011","0.121",{"$nulls":3},"ExAC_FIN_AF",0.0001512,{"$nulls":7},"0/0","359,0","0","359","0/1","374,53","0.1241","427",null,"chr6:116515832:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1246"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FAM49B","chr8:129862322","FAM49B(P70A)",{"$nulls":6},255,"PASS","Missense","rs562871390",7.5642965204236008E-4,{"$nulls":6},"p.Pro70Ala","c.208C>G","MODERATE","70/324",8,{"$nulls":5},"5","378","755","245","480","358","697","0","0","0","0.0832",{"$nulls":20},"3.304838","0.06;0.06;0.06;0.06;0.06;0.06;0.06;.;.;0.06;0.06;0.06;0.06;0.06","2.345;2.345;2.345;2.345;2.345;2.345;2.345;.;.;.;.;.;.;.","1","-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;.;.;-7.48;-7.08;-7.08;-7.08;-6.75","0.628;0.628;0.628;0.628;0.628;0.628;0.628;.;.;.;.;.;.;.","0.024;0.024;0.024;0.024;0.024;0.024;0.024;.;.;0.018;0.026;0.025;0.028;0.032","0.398;0.398;0.398;0.398;0.398;0.398;0.398;0.294;.;.;.;.;.;.",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":7},"0/0","358,0","0","358","0/1","637,66","0.0939","703",null,"chr8:129862322:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0875"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FAM49B","chr8:129862322","FAM49B(P70A)",{"$nulls":6},255,"PASS","Missense","rs562871390",7.5642965204236008E-4,{"$nulls":6},"p.Pro70Ala","c.208C>G","MODERATE","70/324",8,{"$nulls":5},"4","378","635","245","390",null,null,"0","0",{"$nulls":22},"3.304838","0.06;0.06;0.06;0.06;0.06;0.06;0.06;.;.;0.06;0.06;0.06;0.06;0.06","2.345;2.345;2.345;2.345;2.345;2.345;2.345;.;.;.;.;.;.;.","1","-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;-7.36;.;.;-7.48;-7.08;-7.08;-7.08;-6.75","0.628;0.628;0.628;0.628;0.628;0.628;0.628;.;.;.;.;.;.;.","0.024;0.024;0.024;0.024;0.024;0.024;0.024;.;.;0.018;0.026;0.025;0.028;0.032","0.398;0.398;0.398;0.398;0.398;0.398;0.398;0.294;.;.;.;.;.;.",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":7},"0/0","357,0","0","357","0/1","534,38","0.0664","572",null,"chr8:129862322:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0718"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FBRS","chr16:30664381","FBRS(P408T)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},75,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro408Thr","c.1222C>A","MODERATE","408/980",7,{"$nulls":5},"1",{"$nulls":30},"0.937185","1.49",null,"0.99949;0.999968","0.12",null,"0.682","0.246",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","91,0","0","93","0/1","98,8","0.0755","106",null,"chr16:30664381:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0755"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FBXL17","chr5:108224176","FBXL17(Y520S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. {ECO:0000250}.; ",{"$nulls":4},"p.Tyr520Ser","c.1559A>C","MODERATE","520/701",5,{"$nulls":5},"5","373","349","265","229","324","296","0","0","0","0.1622",{"$nulls":20},"2.279541","2.4;2.7;.;2.4",".;0.55;.;.","0.970241;0.970241;0.992409","-1.91;-1.69;.;-1.84",".;0.361;.;0.493","0.39;0.359;.;0.362","0.664;0.676;0.625;0.63",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Members of the F-box protein family, such as FBXL17, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008].  ",null,null,"0/0","350,0","0","350","0/1","277,51","0.1555","328",null,"chr5:108224176:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1528"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FBXL17","chr5:108224176","FBXL17(Y520S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. {ECO:0000250}.; ",{"$nulls":4},"p.Tyr520Ser","c.1559A>C","MODERATE","520/701",5,{"$nulls":5},"4","373","385","265","275",null,null,"0","0",{"$nulls":22},"2.279541","2.4;2.7;.;2.4",".;0.55;.;.","0.970241;0.970241;0.992409","-1.91;-1.69;.;-1.84",".;0.361;.;0.493","0.39;0.359;.;0.362","0.664;0.676;0.625;0.63",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Members of the F-box protein family, such as FBXL17, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008].  ",null,null,"0/0","364,0","0","364","0/1","348,20","0.0543","368",null,"chr5:108224176:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0509"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FGF7","chr15:49424402","FGF7(M35I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays an important role in the regulation of embryonic development, cell proliferation and cell differentiation. Required for normal branching morphogenesis. Growth factor active on keratinocytes. Possible major paracrine effector of normal epithelial cell proliferation. {ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:8663044}.; ","level2",{"$nulls":3},"p.Met35Ile","c.105G>A","MODERATE","35/194",2,{"$nulls":5},"5","423","373","323","280","369","318","0","0","0","0.3616",{"$nulls":20},"2.468837","1.5;.;1.5","1.7","1;1;0.99261;0.99261","-0.44;.;-0.74","0.779;0.779;.","0.123;.;0.148","0.431;0.431;0.344",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kMAPK",{"$nulls":3},"0/0","416,0","0","416","0/1","236,130","0.3552","366",null,"chr15:49424402:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3536"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FGF7","chr15:49424402","FGF7(M35I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays an important role in the regulation of embryonic development, cell proliferation and cell differentiation. Required for normal branching morphogenesis. Growth factor active on keratinocytes. Possible major paracrine effector of normal epithelial cell proliferation. {ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:8663044}.; ","level2",{"$nulls":3},"p.Met35Ile","c.105G>A","MODERATE","35/194",2,{"$nulls":5},"5","423","498","323","370","367","429","0","0","0","0.1259",{"$nulls":20},"2.468837","1.5;.;1.5","1.7","1;1;0.99261;0.99261","-0.44;.;-0.74","0.779;0.779;.","0.123;.;0.148","0.431;0.431;0.344",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kMAPK",{"$nulls":3},"0/0","413,0","0","413","0/1","418,65","0.1346","483",null,"chr15:49424402:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1378"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FHL5","chr6:96606025","FHL5(P153L)",null,null,"domain (LIM zinc-binding 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in the regulation of spermatogenesis. Stimulates CREM transcriptional activity in a phosphorylation- independent manner. {ECO:0000269|PubMed:11327716}.; ",{"$nulls":4},"p.Pro153Leu","c.458C>T","MODERATE","153/284",5,{"$nulls":5},"4","486","509","322","329","458","461","0","0","0","0.1236",{"$nulls":20},"2.854891","-2.25","2.37;.;2.37","1","-7.62;-8.12;-7.62","0.726;.;0.726","0.002;0.003;0.002","0.51;.;0.481",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","476,0","0","476","0/1","428,64","0.1301","492",null,"chr6:96606025:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1368"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FHL5","chr6:96606025","FHL5(P153L)",null,null,"domain (LIM zinc-binding 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in the regulation of spermatogenesis. Stimulates CREM transcriptional activity in a phosphorylation- independent manner. {ECO:0000269|PubMed:11327716}.; ",{"$nulls":4},"p.Pro153Leu","c.458C>T","MODERATE","153/284",5,{"$nulls":5},"4","486","571","322","380","456","511","0","0","0","0.0763",{"$nulls":20},"2.854891","-2.25","2.37;.;2.37","1","-7.62;-8.12;-7.62","0.726;.;0.726","0.002;0.003;0.002","0.51;.;0.481",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","474,0","0","474","0/1","510,43","0.0778","553",null,"chr6:96606025:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0816"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FLNC","chr7:128848005","FLNC(T1506S)",null,null,"repeat (Filamin 13 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Myopathy, myofibrillar, 5 (MFM5) [MIM:609524]: A form of myofibrillar myopathy, a group of chronic neuromuscular disorders characterized at ultrastructural level by disintegration of the sarcomeric Z disk and myofibrils, and replacement of the normal myofibrillar markings by small dense granules, or larger hyaline masses, or amorphous material. MFM5 is characterized by onset in adulthood, clinical features of a limb-girdle myopathy, and focal myofibrillar destruction. {ECO:0000269|PubMed:15929027}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myopathy, distal, 4 (MPD4) [MIM:614065]: A slowly progressive muscular disorder characterized by distal muscle weakness and atrophy affecting the upper and lower limbs. Onset occurs around the third to fourth decades of life, and patients remain ambulatory even after long disease duration. Muscle biopsy shows non-specific changes with no evidence of rods, necrosis, or inflammation. {ECO:0000269|PubMed:21620354}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 26 (CMH26) [MIM:617047]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:25351925}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial restrictive 5 (RCM5) [MIM:617047]: A heart disorder characterized by impaired filling of the ventricles with reduced diastolic volume, in the presence of normal or near normal wall thickness and systolic function. {ECO:0000269|PubMed:26666891}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Muscle-specific filamin, which plays a central role in muscle cells, probably by functioning as a large actin-cross- linking protein. May be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. Critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers.; ","level2",{"$nulls":3},"p.Thr1506Ser","c.4517C>G","MODERATE","1506/2725",26,{"$nulls":5},"4","1040","1100","752","805","911","986","0","0","0","0.2444",{"$nulls":20},"2.401025","-0.85","2.335","0.989255","-1.97;-1.94","0.153;0.208","0.085;0.086","0.574;0.579",{"$nulls":3},"Unknown",-1,"AD","Myopathy, distal, 4; Myopathy, myofibrillar, 5","Cardiovascular; Musculoskeletal","kMAPK","This gene encodes one of three related filamin genes, specifically gamma filamin. These filamin proteins crosslink actin filaments into orthogonal networks in cortical cytoplasm and participate in the anchoring of membrane proteins for the actin cytoskeleton. Three functional domains exist in filamin: an N-terminal filamentous actin-binding domain, a C-terminal self-association domain, and a membrane glycoprotein-binding domain. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].",null,"C1836050| C3279722| C4310749","0/0","1011,0","0","1011","0/1","801,267","0.25","1068",null,"chr7:128848005:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2497"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FLNC","chr7:128848005","FLNC(T1506S)",null,null,"repeat (Filamin 13 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Myopathy, myofibrillar, 5 (MFM5) [MIM:609524]: A form of myofibrillar myopathy, a group of chronic neuromuscular disorders characterized at ultrastructural level by disintegration of the sarcomeric Z disk and myofibrils, and replacement of the normal myofibrillar markings by small dense granules, or larger hyaline masses, or amorphous material. MFM5 is characterized by onset in adulthood, clinical features of a limb-girdle myopathy, and focal myofibrillar destruction. {ECO:0000269|PubMed:15929027}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myopathy, distal, 4 (MPD4) [MIM:614065]: A slowly progressive muscular disorder characterized by distal muscle weakness and atrophy affecting the upper and lower limbs. Onset occurs around the third to fourth decades of life, and patients remain ambulatory even after long disease duration. Muscle biopsy shows non-specific changes with no evidence of rods, necrosis, or inflammation. {ECO:0000269|PubMed:21620354}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 26 (CMH26) [MIM:617047]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:25351925}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial restrictive 5 (RCM5) [MIM:617047]: A heart disorder characterized by impaired filling of the ventricles with reduced diastolic volume, in the presence of normal or near normal wall thickness and systolic function. {ECO:0000269|PubMed:26666891}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Muscle-specific filamin, which plays a central role in muscle cells, probably by functioning as a large actin-cross- linking protein. May be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. Critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers.; ","level2",{"$nulls":3},"p.Thr1506Ser","c.4517C>G","MODERATE","1506/2725",26,{"$nulls":5},"4","1040","1261","752","909","913","1122","0","0","0","0.1096",{"$nulls":20},"2.401025","-0.85","2.335","0.989255","-1.97;-1.94","0.153;0.208","0.085;0.086","0.574;0.579",{"$nulls":3},"Unknown",-1,"AD","Myopathy, distal, 4; Myopathy, myofibrillar, 5","Cardiovascular; Musculoskeletal","kMAPK","This gene encodes one of three related filamin genes, specifically gamma filamin. These filamin proteins crosslink actin filaments into orthogonal networks in cortical cytoplasm and participate in the anchoring of membrane proteins for the actin cytoskeleton. Three functional domains exist in filamin: an N-terminal filamentous actin-binding domain, a C-terminal self-association domain, and a membrane glycoprotein-binding domain. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].",null,"C1836050| C3279722| C4310749","0/0","992,0","0","992","0/1","1048,144","0.1208","1192",null,"chr7:128848005:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1111"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FMO1","chr1:171282168","FMO1(E340Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides. Form I catalyzes the N-oxygenation of secondary and tertiary amines.; ",{"$nulls":4},"p.Glu340Gln","c.1018G>C","MODERATE","340/532",6,{"$nulls":5},"4","621","774","440","560","548","678","0","0","0","0.1386",{"$nulls":20},"3.837365","0.29;.;0.29;0.29",".;2.235;2.235;2.235","0.991085","-1.93;.;-2.06;-2.06",".;0.996;0.996;0.996","0.005;.;0.008;0.008","0.291;0.282;0.28;0.263",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","592,0","0","592","0/1","641,105","0.1408","746",null,"chr1:171282168:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.125"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FMO1","chr1:171282168","FMO1(E340Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides. Form I catalyzes the N-oxygenation of secondary and tertiary amines.; ",{"$nulls":4},"p.Glu340Gln","c.1018G>C","MODERATE","340/532",6,{"$nulls":5},"3","621","848","440","605",null,null,"0","0",{"$nulls":22},"3.837365","0.29;.;0.29;0.29",".;2.235;2.235;2.235","0.991085","-1.93;.;-2.06;-2.06",".;0.996;0.996;0.996","0.005;.;0.008;0.008","0.291;0.282;0.28;0.263",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","589,0","0","589","0/1","750,46","0.0578","796",null,"chr1:171282168:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0628"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FOCAD","chr9:20944742","FOCAD(D1175H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential tumor suppressor in gliomas. {ECO:0000250, ECO:0000269|PubMed:22427331}.; ",{"$nulls":4},"p.Asp1175His","c.3523G>C","MODERATE","1175/1801",28,{"$nulls":5},"5","407","379","275","264","379","350","0","0","0","0.1343",{"$nulls":20},"3.742239","-0.27;-0.27;.;.;.",null,"0.890521","-2.21;-2.21;.;.;.",null,"0.003;0.003;.;.;.","0.408;0.414;0.403;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","399,0","0","399","0/1","319,57","0.1516","376",null,"chr9:20944742:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1591"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FOCAD","chr9:20944742","FOCAD(D1175H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential tumor suppressor in gliomas. {ECO:0000250, ECO:0000269|PubMed:22427331}.; ",{"$nulls":4},"p.Asp1175His","c.3523G>C","MODERATE","1175/1801",28,{"$nulls":5},"5","407","473","275","339","377","446","0","0","0","0.0516",{"$nulls":20},"3.742239","-0.27;-0.27;.;.;.",null,"0.890521","-2.21;-2.21;.;.;.",null,"0.003;0.003;.;.;.","0.408;0.414;0.403;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","400,0","0","400","0/1","435,26","0.0564","461",null,"chr9:20944742:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.056"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FOXO6","chr1:41382839","FOXO6(E546D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator. {ECO:0000250}.; ",{"$nulls":4},"p.Glu546Asp","c.1638G>C","MODERATE","546/559",2,{"$nulls":5},"5","111","114","82","92","89","93","0","0","0","0.0753",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","102,0","0","102","0/1","98,12","0.1091","110",null,"chr1:41382839:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0978"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FOXO6","chr1:41382839","FOXO6(E546D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator. {ECO:0000250}.; ",{"$nulls":4},"p.Glu546Asp","c.1638G>C","MODERATE","546/559",2,{"$nulls":5},"5","111","102","82","86","89","86","0","0","0","0.0581",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","103,0","0","103","0/1","93,6","0.0606","99",null,"chr1:41382839:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0581"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","FRAS1","chr4:78429157","FRAS1(Q1592*)",null,null,"topological domain (Extracellular ), splice variant (In isoform 4. ), splice variant (In isoform 6. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Fraser syndrome 1 (FRASRS1) [MIM:219000]: A form of Fraser syndrome, an autosomal recessive disorder characterized by cryptophthalmos, cutaneous syndactyly, and urogenital abnormalities including renal agenesis or hypoplasia. Additional features include abnormalities of the larynx, ear malformations, and facial abnormalities. {ECO:0000269|PubMed:12766769, ECO:0000269|PubMed:23473829}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ",{"$nulls":5},"p.Gln1592*","c.4774C>T","HIGH","1592/4012",36,1,{"$nulls":4},"5","499","620","350","434","367","452","0","0","0","0.1195",{"$nulls":5},"(FRAS1|ENSG00000138759|1|1.00)","(FRAS1|ENSG00000138759|1|1.00)",{"$nulls":13},"6.292828",null,null,"1",{"$nulls":3},"0.868;0.829",{"$nulls":3},"Unknown",-1,"AR","Fraser syndrome","Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C4551480","0/0","471,0","0","471","0/1","506,75","0.1291","581",null,"chr4:78429157:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1221"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","FRAS1","chr4:78429157","FRAS1(Q1592*)",null,null,"topological domain (Extracellular ), splice variant (In isoform 4. ), splice variant (In isoform 6. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Fraser syndrome 1 (FRASRS1) [MIM:219000]: A form of Fraser syndrome, an autosomal recessive disorder characterized by cryptophthalmos, cutaneous syndactyly, and urogenital abnormalities including renal agenesis or hypoplasia. Additional features include abnormalities of the larynx, ear malformations, and facial abnormalities. {ECO:0000269|PubMed:12766769, ECO:0000269|PubMed:23473829}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ",{"$nulls":5},"p.Gln1592*","c.4774C>T","HIGH","1592/4012",36,1,{"$nulls":4},"5","499","568","350","380","366","426","0","0","0","0.0657",{"$nulls":5},"(FRAS1|ENSG00000138759|1|1.00)","(FRAS1|ENSG00000138759|1|1.00)",{"$nulls":13},"6.292828",null,null,"1",{"$nulls":3},"0.868;0.829",{"$nulls":3},"Unknown",-1,"AR","Fraser syndrome","Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C4551480","0/0","475,0","0","475","0/1","491,33","0.063","524",null,"chr4:78429157:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0579"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GALNT11","chr7:152100821","GALNT11(Q107E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Defects in GALNT11 may be a cause of heterotaxy, a congenital heart disease resulting from abnormalities in left- right (LR) body patterning. {ECO:0000269|PubMed:21282601}.; ","FUNCTION: Polypeptide N-acetylgalactosaminyltransferase that catalyzes the initiation of protein O-linked glycosylation and is involved in left/right asymmetry by mediating O-glycosylation of NOTCH1. O-glycosylation of NOTCH1 promotes activation of NOTCH1, modulating the balance between motile and immotile (sensory) cilia at the left-right organiser (LRO). Polypeptide N- acetylgalactosaminyltransferases catalyze the transfer of an N- acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Displays the same enzyme activity toward MUC1, MUC4, and EA2 than GALNT1. Not involved in glycosylation of erythropoietin (EPO). {ECO:0000269|PubMed:11925450, ECO:0000269|PubMed:24226769}.; ",{"$nulls":4},"p.Gln107Glu","c.319C>G","MODERATE","107/608",3,{"$nulls":5},"5","422","511","304","366","356","432","0","0","0","0.0995",{"$nulls":20},"2.625166","-2.55;-2.55;-2.55;.;-2.55;-2.55","2.485;2.485;2.485;2.485;.;.","1","-1.63;-1.63;-1.67;.;-1.67;-1.5","0.075;0.075;0.893;0.893;.;.","0.016;0.016;0.007;.;0.01;0.012","0.635;0.622;0.624;0.622;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","388,0","0","388","0/1","419,46","0.0989","465",null,"chr7:152100821:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1038"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GAPVD1","chr9:125298929","GAPVD1(K3T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts both as a GTPase-activating protein (GAP) and a guanine nucleotide exchange factor (GEF), and participates in various processes such as endocytosis, insulin receptor internalization or LC2A4/GLUT4 trafficking. Acts as a GEF for the Ras-related protein RAB31 by exchanging bound GDP for free GTP, leading to regulate LC2A4/GLUT4 trafficking. In the absence of insulin, it maintains RAB31 in an active state and promotes a futile cycle between LC2A4/GLUT4 storage vesicles and early endosomes, retaining LC2A4/GLUT4 inside the cells. Upon insulin stimulation, it is translocated to the plasma membrane, releasing LC2A4/GLUT4 from intracellular storage vesicles. Also involved in EGFR trafficking and degradation, possibly by promoting EGFR ubiquitination and subsequent degradation by the proteasome. Has GEF activity for Rab5 and GAP activity for Ras. {ECO:0000269|PubMed:16410077}.; ",{"$nulls":4},"p.Lys3Thr","c.8A>C","MODERATE","3/1487",2,{"$nulls":5},"4","97","127",null,null,"74","95","0","0","0","0.2",{"$nulls":20},"3.727463",null,".;.;0.69;0.69;.;0.69;.;0.69;0.69;0.69","0.999999","-1.99;-1.67;-1.26;-1.26;-1.26;-1.26;-1.57;-1.26;-1.26;-1.26",".;0.967;0.989;0.989;.;0.981;.;0.989;0.981;0.989","0.017;0.007;0.007;0.009;0.008;0.006;0.007;0.008;0.006;0.008",".;0.735;0.642;0.744;0.791;0.766;.;0.738;0.723;0.716",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","96,0","0","96","0/1","108,19","0.1496","127",null,"chr9:125298929:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GAPVD1","chr9:125298929","GAPVD1(K3T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts both as a GTPase-activating protein (GAP) and a guanine nucleotide exchange factor (GEF), and participates in various processes such as endocytosis, insulin receptor internalization or LC2A4/GLUT4 trafficking. Acts as a GEF for the Ras-related protein RAB31 by exchanging bound GDP for free GTP, leading to regulate LC2A4/GLUT4 trafficking. In the absence of insulin, it maintains RAB31 in an active state and promotes a futile cycle between LC2A4/GLUT4 storage vesicles and early endosomes, retaining LC2A4/GLUT4 inside the cells. Upon insulin stimulation, it is translocated to the plasma membrane, releasing LC2A4/GLUT4 from intracellular storage vesicles. Also involved in EGFR trafficking and degradation, possibly by promoting EGFR ubiquitination and subsequent degradation by the proteasome. Has GEF activity for Rab5 and GAP activity for Ras. {ECO:0000269|PubMed:16410077}.; ",{"$nulls":4},"p.Lys3Thr","c.8A>C","MODERATE","3/1487",2,{"$nulls":5},"3",null,null,"85","91",{"$nulls":26},"3.727463",null,".;.;0.69;0.69;.;0.69;.;0.69;0.69;0.69","0.999999","-1.99;-1.67;-1.26;-1.26;-1.26;-1.26;-1.57;-1.26;-1.26;-1.26",".;0.967;0.989;0.989;.;0.981;.;0.989;0.981;0.989","0.017;0.007;0.007;0.009;0.008;0.006;0.007;0.008;0.006;0.008",".;0.735;0.642;0.744;0.791;0.766;.;0.738;0.723;0.716",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","97,0","0","97","0/1","90,7","0.0722","97",null,"chr9:125298929:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0769"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GET4","chr7:893917","GET4(Q281K)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: As part of a cytosolic protein quality control complex, the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and participates to their proper delivery to the endoplasmic reticulum or alternatively can promote their sorting to the proteasome where they undergo degradation (PubMed:20676083, PubMed:21636303, PubMed:21743475, PubMed:28104892). The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane. Recruited to ribosomes, it interacts with the transmembrane region of newly synthesized tail-anchored proteins and together with SGTA and ASNA1 mediates their delivery to the endoplasmic reticulum (PubMed:20676083, PubMed:28104892, PubMed:25535373). Client proteins that cannot be properly delivered to the endoplasmic reticulum are ubiquitinated and sorted to the proteasome (PubMed:28104892). Similarly, the BAG6/BAT3 complex also functions as a sorting platform for proteins of the secretory pathway that are mislocalized to the cytosol either delivering them to the proteasome for degradation or to the endoplasmic reticulum (PubMed:21743475). The BAG6/BAT3 complex also plays a role in the endoplasmic reticulum-associated degradation (ERAD), a quality control mechanism that eliminates unwanted proteins of the endoplasmic reticulum through their retrotranslocation to the cytosol and their targeting to the proteasome. It maintains these retrotranslocated proteins in an unfolded yet soluble state condition in the cytosol to ensure their proper delivery to the proteasome (PubMed:21636303). {ECO:0000269|PubMed:20676083, ECO:0000269|PubMed:21636303, ECO:0000269|PubMed:21743475, ECO:0000269|PubMed:25535373, ECO:0000269|PubMed:28104892}.; ",{"$nulls":4},"p.Gln281Lys","c.841C>A","MODERATE","281/327",8,2,{"$nulls":4},"4","827","898","587","646","770","812","0","0","0","0.101",{"$nulls":20},"3.437563","-0.8;.","2.52;.","1","-2.66;-2.76","1.0;.","0.094;0.038","0.814;0.818",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","796,0","0","796","0/1","752,110","0.1276","862",null,"chr7:893917:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1269"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GET4","chr7:893917","GET4(Q281K)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: As part of a cytosolic protein quality control complex, the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and participates to their proper delivery to the endoplasmic reticulum or alternatively can promote their sorting to the proteasome where they undergo degradation (PubMed:20676083, PubMed:21636303, PubMed:21743475, PubMed:28104892). The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane. Recruited to ribosomes, it interacts with the transmembrane region of newly synthesized tail-anchored proteins and together with SGTA and ASNA1 mediates their delivery to the endoplasmic reticulum (PubMed:20676083, PubMed:28104892, PubMed:25535373). Client proteins that cannot be properly delivered to the endoplasmic reticulum are ubiquitinated and sorted to the proteasome (PubMed:28104892). Similarly, the BAG6/BAT3 complex also functions as a sorting platform for proteins of the secretory pathway that are mislocalized to the cytosol either delivering them to the proteasome for degradation or to the endoplasmic reticulum (PubMed:21743475). The BAG6/BAT3 complex also plays a role in the endoplasmic reticulum-associated degradation (ERAD), a quality control mechanism that eliminates unwanted proteins of the endoplasmic reticulum through their retrotranslocation to the cytosol and their targeting to the proteasome. It maintains these retrotranslocated proteins in an unfolded yet soluble state condition in the cytosol to ensure their proper delivery to the proteasome (PubMed:21636303). {ECO:0000269|PubMed:20676083, ECO:0000269|PubMed:21636303, ECO:0000269|PubMed:21743475, ECO:0000269|PubMed:25535373, ECO:0000269|PubMed:28104892}.; ",{"$nulls":4},"p.Gln281Lys","c.841C>A","MODERATE","281/327",8,2,{"$nulls":4},"4","827","965","587","657","772","889","0","0","0","0.0945",{"$nulls":20},"3.437563","-0.8;.","2.52;.","1","-2.66;-2.76","1.0;.","0.094;0.038","0.814;0.818",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","806,0","0","806","0/1","828,106","0.1135","934",null,"chr7:893917:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1111"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GFI1","chr1:92483371","GFI1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Neutropenia, severe congenital 2, autosomal dominant (SCN2) [MIM:613107]: A disorder of hematopoiesis characterized by maturation arrest of granulopoiesis at the level of promyelocytes with peripheral blood absolute neutrophil counts below 0.5 x 10(9)/l and early onset of severe bacterial infections. {ECO:0000269|PubMed:12778173}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dominant nonimmune chronic idiopathic neutropenia of adults (NI-CINA) [MIM:607847]: Relatively mild form of neutropenia diagnosed in adults, but predisposing to leukemia in a subset of patients. {ECO:0000269|PubMed:12778173}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription repressor essential for hematopoiesis. Functions in a cell-context and development-specific manner. Binds to 5'-TAAATCAC[AT]GCA-3' in the promoter region of a large number of genes. Component of several complexes, including the EHMT2- GFI1-HDAC1, AJUBA-GFI1-HDAC1 and RCOR-GFI-KDM1A-HDAC complexes, that suppress, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Regulates neutrophil differentiation, promotes proliferation of lymphoid cells, and is required for granulocyte development. Mediates, together with U2AF1L4, the alternative splicing of CD45 and controls T-cell receptor signaling. Regulates the endotoxin- mediated Toll-like receptor (TLR) inflammatory response by antagonizing RELA. Cooperates with CBFA2T2 to regulate ITGB1- dependent neurite growth. Controls cell-cycle progression by repressing CDKNIA/p21 transcription in response to TGFB1 via recruitment of GFI1 by ZBTB17 to the CDKNIA/p21 and CDKNIB promoters. Required for the maintenance of inner ear hair cells. {ECO:0000269|PubMed:11060035, ECO:0000269|PubMed:12778173, ECO:0000269|PubMed:16287849, ECO:0000269|PubMed:17197705, ECO:0000269|PubMed:17646546, ECO:0000269|PubMed:18805794, ECO:0000269|PubMed:19026687, ECO:0000269|PubMed:19164764, ECO:0000269|PubMed:20190815, ECO:0000269|PubMed:20547752, ECO:0000269|PubMed:8754800}.; ",{"$nulls":5},"c.115+2T>G","HIGH",null,2,{"$nulls":5},"5","249","246","200","205","188","185","0","0","0","0.1676",{"$nulls":5},"(GFI1|ENSG00000162676|1|1.00)",{"$nulls":14},"5.171089",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Neutropenia, severe congenital, 2 autosomal dominant; Neutropenia, nonimmune chronic idiopathic, of adults ","Allergy/Immunology/Infectious; Oncologic",{"$nulls":3},"C1842930| C2751288","0/0","245,0","0","245","0/1","204,36","0.15","240",null,"chr1:92483371:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1463"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GFI1","chr1:92483371","GFI1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Neutropenia, severe congenital 2, autosomal dominant (SCN2) [MIM:613107]: A disorder of hematopoiesis characterized by maturation arrest of granulopoiesis at the level of promyelocytes with peripheral blood absolute neutrophil counts below 0.5 x 10(9)/l and early onset of severe bacterial infections. {ECO:0000269|PubMed:12778173}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dominant nonimmune chronic idiopathic neutropenia of adults (NI-CINA) [MIM:607847]: Relatively mild form of neutropenia diagnosed in adults, but predisposing to leukemia in a subset of patients. {ECO:0000269|PubMed:12778173}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription repressor essential for hematopoiesis. Functions in a cell-context and development-specific manner. Binds to 5'-TAAATCAC[AT]GCA-3' in the promoter region of a large number of genes. Component of several complexes, including the EHMT2- GFI1-HDAC1, AJUBA-GFI1-HDAC1 and RCOR-GFI-KDM1A-HDAC complexes, that suppress, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Regulates neutrophil differentiation, promotes proliferation of lymphoid cells, and is required for granulocyte development. Mediates, together with U2AF1L4, the alternative splicing of CD45 and controls T-cell receptor signaling. Regulates the endotoxin- mediated Toll-like receptor (TLR) inflammatory response by antagonizing RELA. Cooperates with CBFA2T2 to regulate ITGB1- dependent neurite growth. Controls cell-cycle progression by repressing CDKNIA/p21 transcription in response to TGFB1 via recruitment of GFI1 by ZBTB17 to the CDKNIA/p21 and CDKNIB promoters. Required for the maintenance of inner ear hair cells. {ECO:0000269|PubMed:11060035, ECO:0000269|PubMed:12778173, ECO:0000269|PubMed:16287849, ECO:0000269|PubMed:17197705, ECO:0000269|PubMed:17646546, ECO:0000269|PubMed:18805794, ECO:0000269|PubMed:19026687, ECO:0000269|PubMed:19164764, ECO:0000269|PubMed:20190815, ECO:0000269|PubMed:20547752, ECO:0000269|PubMed:8754800}.; ",{"$nulls":5},"c.115+2T>G","HIGH",null,2,{"$nulls":5},"5","249","309","200","245","189","233","0","0","0","0.1245",{"$nulls":5},"(GFI1|ENSG00000162676|1|1.00)",{"$nulls":14},"5.171089",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Neutropenia, severe congenital, 2 autosomal dominant; Neutropenia, nonimmune chronic idiopathic, of adults ","Allergy/Immunology/Infectious; Oncologic",{"$nulls":3},"C1842930| C2751288","0/0","245,0","0","245","0/1","272,33","0.1082","305",null,"chr1:92483371:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1061"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GLI4","chr8:143274739","GLI4(P54T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro54Thr","c.160C>A","MODERATE","54/376",3,{"$nulls":5},"5","641","1166","514","923","467","854","0","0","0","0.0855",{"$nulls":20},"0.150473",".;3.36;.;3.36;.;.",".;0.345;.;0.345;.;.","0.999994;0.999994;0.999998;0.999994;0.999994","-4.36;-0.54;-4.36;-0.54;-4.36;-4.36",".;0.001;.;0.001;.;.","0.1;0.138;0.289;0.138;0.15;0.218","0.083;0.109;0.029;0.131;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","607,0","0","607","0/1","1048,87","0.0767","1135",null,"chr8:143274739:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0704"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GLIPR1L2","chr12:75410604","GLIPR1L2(R135S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg135Ser","c.405A>T","MODERATE","135/344",2,{"$nulls":5},"5","371","541","262","376","331","489","0","0","0","0.0982",{"$nulls":20},"2.014529","3.19","1.345;.;1.345;1.345","0.94537","-0.82;-0.87;-0.91;-1.14","0.626;.;0.05;.","0.332;0.157;0.649;0.702","0.312;0.32;0.326;0.318",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","357,0","0","357","0/1","468,57","0.1086","525",null,"chr12:75410604:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1064"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GLTSCR1","chr19:47694464","GLTSCR1(H878P)",{"$nulls":6},88,"PASS","Missense","rs867528906",-1,{"$nulls":6},"p.His878Pro","c.2633A>C","MODERATE","878/1560",8,7,{"$nulls":4},"1",{"$nulls":30},"1.459651","1.41;.",null,"0.992629","-0.89;.","0.938;.","0.02;.","0.321;0.369",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","149,0","0","149","0/1","72,12","0.1429","84",null,"chr19:47694464:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1429"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GNA11","chr19:3113383","GNA11(E125D)",null,null,"domain (G-alpha )",{"$nulls":3},255,"PASS","Missense","rs1165709212",-1,"DISEASE: Hypocalciuric hypercalcemia, familial 2 (HHC2) [MIM:145981]: A form of hypocalciuric hypercalcemia, a disorder of mineral homeostasis that is transmitted as an autosomal dominant trait with a high degree of penetrance. It is characterized biochemically by lifelong elevation of serum calcium concentrations and is associated with inappropriately low urinary calcium excretion and a normal or mildly elevated circulating parathyroid hormone level. Hypermagnesemia is typically present. Affected individuals are usually asymptomatic and the disorder is considered benign. However, chondrocalcinosis and pancreatitis occur in some adults. {ECO:0000269|PubMed:23802516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypocalcemia, autosomal dominant 2 (HYPOC2) [MIM:615361]: A form of hypocalcemia, a disorder of mineral homeostasis characterized by blood calcium levels below normal, and low or normal serum parathyroid hormone concentrations. Disease manifestations include hypocalcemia, paresthesias, carpopedal spasm, seizures, hypercalciuria with nephrocalcinosis or kidney stones, and ectopic and basal ganglia calcifications. {ECO:0000269|PubMed:23782177, ECO:0000269|PubMed:23802516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. Acts as an activator of phospholipase C.; ","gedi|foundationOne|illumina|level2","[ \"Dabrafenib\" , \"Trametinib\" , \"Vemurafenib\"]","[ \"Dabrafenib\" , \"Trametinib\" , \"Vemurafenib\"]","[ \"Dabrafenib\" , \"Trametinib\" , \"Vemurafenib\"]","p.Glu125Asp","c.375G>C","MODERATE","125/359",3,{"$nulls":5},"5","607","376","430","281","503","322","0","0","0","0.1894",{"$nulls":20},"2.065811","-2.43","0.265","0.999929","-1.36",null,"0.196","0.495",{"$nulls":3},"Unknown",-1,"AD","Hypocalcemia 2, autosomal dominant; Hypocalciuric hypercalcemia, autosomal dominant","Endocrine","COSMIC",null,null,"C3809243| C1840347","0/0","574,0","0","574","0/1","300,65","0.1781","365",null,"chr19:3113383:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1851"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GNA11","chr19:3113383","GNA11(E125D)",null,null,"domain (G-alpha )",{"$nulls":3},255,"PASS","Missense","rs1165709212",-1,"DISEASE: Hypocalciuric hypercalcemia, familial 2 (HHC2) [MIM:145981]: A form of hypocalciuric hypercalcemia, a disorder of mineral homeostasis that is transmitted as an autosomal dominant trait with a high degree of penetrance. It is characterized biochemically by lifelong elevation of serum calcium concentrations and is associated with inappropriately low urinary calcium excretion and a normal or mildly elevated circulating parathyroid hormone level. Hypermagnesemia is typically present. Affected individuals are usually asymptomatic and the disorder is considered benign. However, chondrocalcinosis and pancreatitis occur in some adults. {ECO:0000269|PubMed:23802516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypocalcemia, autosomal dominant 2 (HYPOC2) [MIM:615361]: A form of hypocalcemia, a disorder of mineral homeostasis characterized by blood calcium levels below normal, and low or normal serum parathyroid hormone concentrations. Disease manifestations include hypocalcemia, paresthesias, carpopedal spasm, seizures, hypercalciuria with nephrocalcinosis or kidney stones, and ectopic and basal ganglia calcifications. {ECO:0000269|PubMed:23782177, ECO:0000269|PubMed:23802516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. Acts as an activator of phospholipase C.; ","gedi|foundationOne|illumina|level2","[ \"Dabrafenib\" , \"Trametinib\" , \"Vemurafenib\"]","[ \"Dabrafenib\" , \"Trametinib\" , \"Vemurafenib\"]","[ \"Dabrafenib\" , \"Trametinib\" , \"Vemurafenib\"]","p.Glu125Asp","c.375G>C","MODERATE","125/359",3,{"$nulls":5},"5","607","530","430","383","503","443","0","0","0","0.0835",{"$nulls":20},"2.065811","-2.43","0.265","0.999929","-1.36",null,"0.196","0.495",{"$nulls":3},"Unknown",-1,"AD","Hypocalcemia 2, autosomal dominant; Hypocalciuric hypercalcemia, autosomal dominant","Endocrine","COSMIC",null,null,"C3809243| C1840347","0/0","587,0","0","587","0/1","472,41","0.0799","513",null,"chr19:3113383:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0836"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GPATCH2L","chr14:76178043","GPATCH2L(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss","rs537955510",7.5642965204236008E-4,{"$nulls":7},"c.1107+1G>T","HIGH",null,7,{"$nulls":5},"4","534","486","358","333","483","440","0","0","0","0.0841",{"$nulls":5},"(GPATCH2L|ENSG00000089916|1|1.00)",{"$nulls":14},"5.076544",null,null,"1",{"$nulls":7},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":7},"0/0","506,1","0.002","507","0/1","406,41","0.0917","447",null,"chr14:76178043:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0961"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GPR162","chr12:6824550","GPR162(RV218CG)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},77,"PASS","Missense",null,-1,null,"FUNCTION: Orphan receptor.; ",{"$nulls":4},"p.ArgVal218CysGly","c.652_656delAGAGTinsTGTGG","MODERATE","218/588",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","148,0","0","158","0/1","95,7","0.0636","110",null,"chr12:6824550:AGAGT:TGTGG",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0636"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GPR182","chr12:56995632","GPR182(I141M)",null,null,"transmembrane region (Helical; Name=3 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Orphan receptor.; ",{"$nulls":4},"p.Ile141Met","c.423C>G","MODERATE","141/404",2,{"$nulls":5},"5","530","485","417","372","433","393","0","0","0","0.2163",{"$nulls":20},"2.591532","-1.01","3.06","0.621205","-2.41","0.999","0.003","0.444",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","497,0","0","497","0/1","372,95","0.2034","467",null,"chr12:56995632:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1962"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GPR182","chr12:56995632","GPR182(I141M)",null,null,"transmembrane region (Helical; Name=3 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Orphan receptor.; ",{"$nulls":4},"p.Ile141Met","c.423C>G","MODERATE","141/404",2,{"$nulls":5},"5","530","582","417","453","433","461","0","0","0","0.0911",{"$nulls":20},"2.591532","-1.01","3.06","0.621205","-2.41","0.999","0.003","0.444",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","506,0","0","506","0/1","512,49","0.0873","561",null,"chr12:56995632:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0883"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRAMD4","chr22:46668732","GRAMD4(N325T)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},87,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role as a mediator of E2F1-induced apoptosis in the absence of p53/TP53. {ECO:0000269|PubMed:15565177}.; ",{"$nulls":4},"p.Asn325Thr","c.974A>C","MODERATE","325/578",11,{"$nulls":5},"1",{"$nulls":30},"4.219314","0.94","2.81","0.999998","-3.63","0.99","0.005","0.973",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","101,0","0","101","0/1","128,14","0.0986","142",null,"chr22:46668732:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0986"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRHPR","chr9:37432085","GRHPR(T271R)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Enzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities. Reduces hydroxypyruvate to D-glycerate, glyoxylate to glycolate oxidizes D-glycerate to hydroxypyruvate.; ",{"$nulls":4},"p.Thr271Arg","c.812C>G","MODERATE","271/358",8,{"$nulls":5},"5","420","448","297","305","375","411","0","0","0","0.1071",{"$nulls":20},"3.869736","-1.4;.","2.48;.","1","-5.03;.","1.0;.","0.003;.","0.916;0.91",{"$nulls":3},"Unknown",-1,"AR","Hyperoxaluria, primary, type II","Biochemical; Renal",null,"This gene encodes an enzyme with hydroxypyruvate reductase, glyoxylate reductase, and D-glycerate dehydrogenase enzymatic activities. The enzyme has widespread tissue expression and has a role in metabolism. Type II hyperoxaluria is caused by mutations in this gene. [provided by RefSeq, Jul 2008].  ",null,"C0268165","0/0","397,0","0","397","0/1","378,47","0.1106","425",null,"chr9:37432085:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.118"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GRHPR","chr9:37432085","GRHPR(T271R)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Enzyme with hydroxy-pyruvate reductase, glyoxylate reductase and D-glycerate dehydrogenase enzymatic activities. Reduces hydroxypyruvate to D-glycerate, glyoxylate to glycolate oxidizes D-glycerate to hydroxypyruvate.; ",{"$nulls":4},"p.Thr271Arg","c.812C>G","MODERATE","271/358",8,{"$nulls":5},"4","420","550","297","387",null,null,"0","0",{"$nulls":22},"3.869736","-1.4;.","2.48;.","1","-5.03;.","1.0;.","0.003;.","0.916;0.91",{"$nulls":3},"Unknown",-1,"AR","Hyperoxaluria, primary, type II","Biochemical; Renal",null,"This gene encodes an enzyme with hydroxypyruvate reductase, glyoxylate reductase, and D-glycerate dehydrogenase enzymatic activities. The enzyme has widespread tissue expression and has a role in metabolism. Type II hyperoxaluria is caused by mutations in this gene. [provided by RefSeq, Jul 2008].  ",null,"C0268165","0/0","397,0","0","397","0/1","490,29","0.0559","519",null,"chr9:37432085:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0594"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRIA2","chr4:157336461","GRIA2(G520R)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs753642820",1.507E-5,null,"FUNCTION: Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate. Through complex formation with NSG1, GRIP1 and STX12 controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting (By similarity). {ECO:0000250|UniProtKB:P19491, ECO:0000269|PubMed:20614889}.; ",{"$nulls":4},"p.Gly520Arg","c.1558G>A","MODERATE","520/883",11,2,{"$nulls":4},"4","508","681","408","521","421","567","0","0","0","0.1376",{"$nulls":20},"4.207278","0.91;0.91;.;0.91;0.91",".;.;2.59;2.59;2.59","1","-7.42;-7.42;.;-7.51;-7.51",".;.;.;1.0;0.999","0.0;0.0;.;0.0;0.0","0.973;0.973;.;0.973;0.976",{"$nulls":3},"ExAC_NFE_AF",1.507E-5,{"$nulls":6},"CN283239","0/0","505,0","0","505","0/1","556,93","0.1433","649",null,"chr4:157336461:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1536"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GRIA2","chr4:157336461","GRIA2(G520R)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs753642820",1.507E-5,null,"FUNCTION: Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate. Through complex formation with NSG1, GRIP1 and STX12 controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting (By similarity). {ECO:0000250|UniProtKB:P19491, ECO:0000269|PubMed:20614889}.; ",{"$nulls":4},"p.Gly520Arg","c.1558G>A","MODERATE","520/883",11,2,{"$nulls":4},"3","508","643","408","493",null,null,"0","0",{"$nulls":22},"4.207278","0.91;0.91;.;0.91;0.91",".;.;2.59;2.59;2.59","1","-7.42;-7.42;.;-7.51;-7.51",".;.;.;1.0;0.999","0.0;0.0;.;0.0;0.0","0.973;0.973;.;0.973;0.976",{"$nulls":3},"ExAC_NFE_AF",1.507E-5,{"$nulls":6},"CN283239","0/0","507,0","0","507","0/1","580,38","0.0615","618",null,"chr4:157336461:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0649"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRIK3","chr1:36802041","GRIK3(S857Y)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate >> L-glutamate = quisqualate >> AMPA = NMDA.; ",{"$nulls":4},"p.Ser857Tyr","c.2570C>A","MODERATE","857/919",16,{"$nulls":5},"5","357","544","250","363","335","515","0","0","0","0.1049",{"$nulls":20},"4.011447","2.61","2.73","0.999914","-3.05","0.985","0.002","0.731",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","346,0","0","346","0/1","467,59","0.1122","526",null,"chr1:36802041:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1129"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GRIK3","chr1:36802041","GRIK3(S857Y)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate >> L-glutamate = quisqualate >> AMPA = NMDA.; ",{"$nulls":4},"p.Ser857Tyr","c.2570C>A","MODERATE","857/919",16,{"$nulls":5},"3",{"$nulls":4},"336","484",null,null,"0","0.0537",{"$nulls":20},"4.011447","2.61","2.73","0.999914","-3.05","0.985","0.002","0.731",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","355,0","0","357","0/1","481,29","0.0569","510",null,"chr1:36802041:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRIN2A","chr16:9764905","GRIN2A(K880T)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Epilepsy, focal, with speech disorder and with or without mental retardation (FESD) [MIM:245570]: A highly variable neurologic disorder with features ranging from severe early-onset seizures associated with delayed psychomotor development, persistent speech difficulties, and mental retardation to a more benign entity characterized by childhood onset of mild or asymptomatic seizures associated with transient speech difficulties followed by remission of seizures in adolescence and normal psychomotor development. The disorder encompasses several clinical entities, including Landau-Kleffner syndrome, epileptic encephalopathy with continuous spike and wave during slow-wave sleep, autosomal dominant rolandic epilepsy, mental retardation and speech dyspraxia, and benign epilepsy with centrotemporal spikes. {ECO:0000269|PubMed:20890276, ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23933818, ECO:0000269|PubMed:23933819, ECO:0000269|PubMed:23933820, ECO:0000269|PubMed:24504326, ECO:0000269|PubMed:24903190, ECO:0000269|PubMed:27839871, ECO:0000269|PubMed:27864847, ECO:0000269|PubMed:28095420, ECO:0000269|PubMed:28126851, ECO:0000269|PubMed:28182669}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving GRIN2A has been found in a family with epilepsy and neurodevelopmental defects. Translocation t(16;17)(p13.2;q11.2).; DISEASE: Note=GRIN2A somatic mutations have been frequently found in cutaneous malignant melanoma, suggesting that the glutamate signaling pathway may play a role in the pathogenesis of melanoma. {ECO:0000269|PubMed:21499247, ECO:0000269|PubMed:24455489}.; ","FUNCTION: Component of NMDA receptor complexes that function as heterotetrameric, ligand-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Channel activation requires binding of the neurotransmitter glutamate to the epsilon subunit, glycine binding to the zeta subunit, plus membrane depolarization to eliminate channel inhibition by Mg(2+) (PubMed:8768735, PubMed:26919761, PubMed:26875626, PubMed:28105280). Sensitivity to glutamate and channel kinetics depend on the subunit composition; channels containing GRIN1 and GRIN2A have higher sensitivity to glutamate and faster kinetics than channels formed by GRIN1 and GRIN2B (PubMed:26919761, PubMed:26875626). Contributes to the slow phase of excitatory postsynaptic current, long-term synaptic potentiation, and learning (By similarity). {ECO:0000250|UniProtKB:P35436, ECO:0000250|UniProtKB:Q00959, ECO:0000269|PubMed:26875626, ECO:0000269|PubMed:26919761, ECO:0000269|PubMed:28105280, ECO:0000269|PubMed:8768735}.; ","gedi|foundationOne",{"$nulls":3},"p.Lys880Thr","c.2639A>C","MODERATE","880/1464",13,{"$nulls":5},"4","1331","1868","1002","1374","1237","1689","0","0","0","0.1273",{"$nulls":20},"3.894124","2.62;.;2.65;2.62","2.515;.;2.515;2.515","0.999999","-1.43;.;-1.43;-1.43","0.999;.;.;0.999","0.016;.;0.024;0.016","0.504;.;0.549;0.622",{"$nulls":3},"Unknown",-1,"AD","Epilepsy with neurodevelopmental defects","Neurologic",{"$nulls":3},"C3806402","0/0","1268,0","0","1268","0/1","1494,236","0.1364","1730",null,"chr16:9764905:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1274"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRK1","chr13:113667775","GRK1(I130T)",null,null,"domain (RGS ), region of interest (N-terminal )",{"$nulls":3},255,"PASS","Missense","rs373055452",2.5536261491317672E-4,"DISEASE: Night blindness, congenital stationary, Oguchi type 2 (CSNBO2) [MIM:613411]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. Congenital stationary night blindness Oguchi type is associated with fundus discoloration and abnormally slow dark adaptation. {ECO:0000269|PubMed:17070587, ECO:0000269|PubMed:9020843}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Retina-specific kinase involved in the signal turnoff via phosphorylation of rhodopsin (RHO), the G protein- coupled receptor that initiates the phototransduction cascade. This rapid desensitization is essential for scotopic vision and permits rapid adaptation to changes in illumination. {ECO:0000269|PubMed:15946941}.; ",{"$nulls":4},"p.Ile130Thr","c.389T>C","MODERATE","130/563",1,{"$nulls":5},"5","419","387","316","297","355","348","0","0","0","0.158",{"$nulls":20},"-0.734972","4.63",null,"1","-0.93",null,"0.223","0.052",{"$nulls":3},"ESP6500_AA_AF",2.5536261491317672E-4,"AR","Oguchi disease 2","Ophthalmologic",{"$nulls":3},"C3150678","0/0","412,0","0","412","0/1","322,63","0.1636","385",null,"chr13:113667775:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1751"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GRK1","chr13:113667775","GRK1(I130T)",null,null,"domain (RGS ), region of interest (N-terminal )",{"$nulls":3},255,"PASS","Missense","rs373055452",2.5536261491317672E-4,"DISEASE: Night blindness, congenital stationary, Oguchi type 2 (CSNBO2) [MIM:613411]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. Congenital stationary night blindness Oguchi type is associated with fundus discoloration and abnormally slow dark adaptation. {ECO:0000269|PubMed:17070587, ECO:0000269|PubMed:9020843}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Retina-specific kinase involved in the signal turnoff via phosphorylation of rhodopsin (RHO), the G protein- coupled receptor that initiates the phototransduction cascade. This rapid desensitization is essential for scotopic vision and permits rapid adaptation to changes in illumination. {ECO:0000269|PubMed:15946941}.; ",{"$nulls":4},"p.Ile130Thr","c.389T>C","MODERATE","130/563",1,{"$nulls":5},"5","419","445","316","318","356","389","0","0","0","0.0643",{"$nulls":20},"-0.734972","4.63",null,"1","-0.93",null,"0.223","0.052",{"$nulls":3},"ESP6500_AA_AF",2.5536261491317672E-4,"AR","Oguchi disease 2","Ophthalmologic",{"$nulls":3},"C3150678","0/0","412,0","0","412","0/1","399,30","0.0699","429",null,"chr13:113667775:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0692"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GRK6","chr5:177434034","GRK6(R287W)",null,null,"domain (Protein kinase ), helix ",{"$nulls":3},255,"PASS","Missense","rs777094286",1.597e-05,null,"FUNCTION: Specifically phosphorylates the activated forms of G protein-coupled receptors. Such receptor phosphorylation initiates beta-arrestin-mediated receptor desensitization, internalization, and signaling events leading to their desensitization. Seems to be involved in the desensitization of D2-like dopamine receptors in striatum and chemokine receptor CXCR4 which is critical for CXCL12-induced cell chemotaxis (By similarity). Phosphorylates rhodopsin (RHO) (in vitro) and a non G-protein-coupled receptor: LRP6 during Wnt signaling (in vitro). {ECO:0000250, ECO:0000269|PubMed:19801552, ECO:0000269|PubMed:20048153}.; ",{"$nulls":4},"p.Arg287Trp","c.859C>T","MODERATE","287/589",9,1,{"$nulls":4},"4","246","180","152","126","239","164","0","0","0","0.3232",{"$nulls":20},"3.284693","-0.2","1.675;.;.;1.675;1.675","1","-7.8;-7.8;-7.46;-7.8;-7.8","0.999;1.0;.;.;0.999","0.0","0.887;0.872;0.897;0.857;0.837",{"$nulls":3},"ExAC_NFE_AF",1.597e-05,{"$nulls":7},"0/0","239,0","0","239","0/1","119,59","0.3315","178",null,"chr5:177434034:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3333"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GRK6","chr5:177434034","GRK6(R287W)",null,null,"domain (Protein kinase ), helix ",{"$nulls":3},255,"PASS","Missense","rs777094286",1.597e-05,null,"FUNCTION: Specifically phosphorylates the activated forms of G protein-coupled receptors. Such receptor phosphorylation initiates beta-arrestin-mediated receptor desensitization, internalization, and signaling events leading to their desensitization. Seems to be involved in the desensitization of D2-like dopamine receptors in striatum and chemokine receptor CXCR4 which is critical for CXCL12-induced cell chemotaxis (By similarity). Phosphorylates rhodopsin (RHO) (in vitro) and a non G-protein-coupled receptor: LRP6 during Wnt signaling (in vitro). {ECO:0000250, ECO:0000269|PubMed:19801552, ECO:0000269|PubMed:20048153}.; ",{"$nulls":4},"p.Arg287Trp","c.859C>T","MODERATE","287/589",9,1,{"$nulls":4},"4","246","263","152","177","240","244","0","0","0","0.168",{"$nulls":20},"3.284693","-0.2","1.675;.;.;1.675;1.675","1","-7.8;-7.8;-7.46;-7.8;-7.8","0.999;1.0;.;.;0.999","0.0","0.887;0.872;0.897;0.857;0.837",{"$nulls":3},"ExAC_NFE_AF",1.597e-05,{"$nulls":7},"0/0","236,0","0","236","0/1","208,44","0.1746","252",null,"chr5:177434034:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1977"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","GSC2","chr22:19149002","GSC2(G203R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May have a role in development. May regulate its own transcription. May bind the bicoid consensus sequence TAATCC.; ",{"$nulls":4},"p.Gly203Arg","c.607G>A","MODERATE","203/205",3,{"$nulls":5},"4","561","448","412","335","450","349","0","0","0","0.2063",{"$nulls":20},"2.357663","-2.75","1.06","0.838117","-0.12","0.089","0.14","0.031",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Goosecoidlike (GSCL), a homeodomain-containing gene, resides in the critical region for VCFS/DGS on 22q11. Velocardiofacial syndrome (VCFS) is a developmental disorder characterized by conotruncal heart defects, craniofacial anomalies, and learning disabilities. VCFS is phenotypically related to DiGeorge syndrome (DGS) and both syndromes are associated with hemizygous 22q11 deletions. Because many of the tissues and structures affected in VCFS/DGS derive from the pharyngeal arches of the developing embryo, it is believed that haploinsufficiency of a gene involved in embryonic development may be responsible for its etiology. The gene is expressed in a limited number of adult tissues, as well as in early human development. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","539,1","0.0019","540","0/1","351,80","0.1856","431",null,"chr22:19149002:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.194"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","GSC2","chr22:19149002","GSC2(G203R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May have a role in development. May regulate its own transcription. May bind the bicoid consensus sequence TAATCC.; ",{"$nulls":4},"p.Gly203Arg","c.607G>A","MODERATE","203/205",3,{"$nulls":5},"4","561","540","412","412","448","451","0","0","0","0.122",{"$nulls":20},"2.357663","-2.75","1.06","0.838117","-0.12","0.089","0.14","0.031",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Goosecoidlike (GSCL), a homeodomain-containing gene, resides in the critical region for VCFS/DGS on 22q11. Velocardiofacial syndrome (VCFS) is a developmental disorder characterized by conotruncal heart defects, craniofacial anomalies, and learning disabilities. VCFS is phenotypically related to DiGeorge syndrome (DGS) and both syndromes are associated with hemizygous 22q11 deletions. Because many of the tissues and structures affected in VCFS/DGS derive from the pharyngeal arches of the developing embryo, it is believed that haploinsufficiency of a gene involved in embryonic development may be responsible for its etiology. The gene is expressed in a limited number of adult tissues, as well as in early human development. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","542,0","0","542","0/1","471,57","0.108","528",null,"chr22:19149002:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1092"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HDGF","chr1:156743530","HDGF(Sequence Feature)",{"$nulls":3},"modified-residue:Phosphoserine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,null,"FUNCTION: Heparin-binding protein, with mitogenic activity for fibroblasts. Acts as a transcriptional repressor. {ECO:0000269|PubMed:17974029}.; ",{"$nulls":5},"c.765-75G>T","MODERATE",null,5,{"$nulls":5},"4","278","265","214","205","220","219","0","0","0","0.137",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","250,0","0","250","0/1","212,37","0.1486","249",null,"chr1:156743530:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1366"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HIC1","chr17:2056734","HIC1(L34Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional repressor. Recognizes and binds to the consensus sequence '5-[CG]NG[CG]GGGCA[CA]CC-3'. May act as a tumor suppressor. May be involved in development of head, face, limbs and ventral body wall. Involved in down-regulation of SIRT1 and thereby is involved in regulation of p53/TP53-dependent apoptotic DNA-damage responses. The specific target gene promoter association seems to be depend on corepressors, such as CTBP1 or CTBP2 and MTA1. The regulation of SIRT1 transcription in response to nutrient deprivation seems to involve CTBP1. In cooperation with MTA1 (indicative for an association with the NuRD complex) represses transcription from CCND1/cyclin-D1 and CDKN1C/p57Kip2 specifically in quiescent cells. Involved in regulation of the Wnt signaling pathway probably by association with TCF7L2 and preventing TCF7L2 and CTNNB1 association with promoters of TCF- responsive genes. Seems to repress transcription from E2F1 and ATOH1 which involves ARID1A, indicative for the participation of a distinct SWI/SNF-type chromatin-remodeling complex. Probably represses transcription from ACKR3, FGFBP1 and EFNA1. {ECO:0000269|PubMed:12052894, ECO:0000269|PubMed:15231840, ECO:0000269|PubMed:16269335, ECO:0000269|PubMed:16690027, ECO:0000269|PubMed:16724116, ECO:0000269|PubMed:17213307, ECO:0000269|PubMed:18347096, ECO:0000269|PubMed:19486893, ECO:0000269|PubMed:19525223, ECO:0000269|PubMed:20154726, ECO:0000269|PubMed:20547755}.; ",{"$nulls":4},"p.Leu34Gln","c.101T>A","MODERATE","34/733",2,{"$nulls":5},"5","582","505","438","370","453","412","0","0","0","0.3083",{"$nulls":20},"4.123455",".;1.68;1.68;.;1.68;1.68",".;.;.;.;.;0.55","0.999999",".;.;-4.64;.;.;-4.7",".;.;.;.;.;1.0",".;.;0.0;.;.;0.0",".;.;0.77;0.772;.;0.775",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","566,0","0","566","0/1","339,143","0.2967","482",null,"chr17:2056734:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2838"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","HIC1","chr17:2056734","HIC1(L34Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional repressor. Recognizes and binds to the consensus sequence '5-[CG]NG[CG]GGGCA[CA]CC-3'. May act as a tumor suppressor. May be involved in development of head, face, limbs and ventral body wall. Involved in down-regulation of SIRT1 and thereby is involved in regulation of p53/TP53-dependent apoptotic DNA-damage responses. The specific target gene promoter association seems to be depend on corepressors, such as CTBP1 or CTBP2 and MTA1. The regulation of SIRT1 transcription in response to nutrient deprivation seems to involve CTBP1. In cooperation with MTA1 (indicative for an association with the NuRD complex) represses transcription from CCND1/cyclin-D1 and CDKN1C/p57Kip2 specifically in quiescent cells. Involved in regulation of the Wnt signaling pathway probably by association with TCF7L2 and preventing TCF7L2 and CTNNB1 association with promoters of TCF- responsive genes. Seems to repress transcription from E2F1 and ATOH1 which involves ARID1A, indicative for the participation of a distinct SWI/SNF-type chromatin-remodeling complex. Probably represses transcription from ACKR3, FGFBP1 and EFNA1. {ECO:0000269|PubMed:12052894, ECO:0000269|PubMed:15231840, ECO:0000269|PubMed:16269335, ECO:0000269|PubMed:16690027, ECO:0000269|PubMed:16724116, ECO:0000269|PubMed:17213307, ECO:0000269|PubMed:18347096, ECO:0000269|PubMed:19486893, ECO:0000269|PubMed:19525223, ECO:0000269|PubMed:20154726, ECO:0000269|PubMed:20547755}.; ",{"$nulls":4},"p.Leu34Gln","c.101T>A","MODERATE","34/733",2,{"$nulls":5},"5","582","610","438","451","457","487","0","0","0","0.1643",{"$nulls":20},"4.123455",".;1.68;1.68;.;1.68;1.68",".;.;.;.;.;0.55","0.999999",".;.;-4.64;.;.;-4.7",".;.;.;.;.;1.0",".;.;0.0;.;.;0.0",".;.;0.77;0.772;.;0.775",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","566,0","0","566","0/1","478,105","0.1801","583",null,"chr17:2056734:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1729"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HIPK3","chr11:33347340","HIPK3(D649H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine-protein kinase involved in transcription regulation, apoptosis and steroidogenic gene expression. Phosphorylates JUN and RUNX2. Seems to negatively regulate apoptosis by promoting FADD phosphorylation. Enhances androgen receptor-mediated transcription. May act as a transcriptional corepressor for NK homeodomain transcription factors. The phosphorylation of NR5A1 activates SF1 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation. In osteoblasts, supports transcription activation: phosphorylates RUNX2 that synergizes with SPEN/MINT to enhance FGFR2-mediated activation of the osteocalcin FGF- responsive element (OCFRE). {ECO:0000269|PubMed:14766760, ECO:0000269|PubMed:17210646}.; ",{"$nulls":4},"p.Asp649His","c.1945G>C","MODERATE","649/1215",9,{"$nulls":5},"5","316","502","218","336","267","441","0","0","0","0.1315",{"$nulls":20},"3.976325","0.58;0.57;0.58;0.58","2.215","1","-3.08;-3.06;-3.08;-3.08","0.996;0.989;0.996;0.996","0.001","0.626;0.414;0.62;0.629",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","302,0","0","302","0/1","420,62","0.1286","482",null,"chr11:33347340:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.128"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HIST1H3C","chr6:26045494","HIST1H3C(K28N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glioma (GLM) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269|PubMed:22286216}. Note=The gene represented in this entry is involved in disease pathogenesis. HIST1H3B mutations affecting residue Lys-28 involved in post-translational modifications of histone H3.1 are recurrent in malignant, aggressive gliomas including pediatric non-brain stem glioblastoma and diffuse intrinsic pontine glioma (DIPG) (PubMed:22286216). The mechanism through which mutations lead to tumorigenesis involves altered histone methylation, impaired regulation of Polycomb repressive complex 2 (PRC2) activity, and aberrant epigenetic regulation of gene expression (PubMed:23603901). {ECO:0000269|PubMed:22286216, ECO:0000269|PubMed:23603901}.; DISEASE: Note=HIST1H3B or HIST1H3C mutations affecting residue Lys-37 of histone H3.1 are involved in the pathogenesis of pediatric undifferentiated soft tissue sarcomas. The mechanism through which mutations lead to tumorigenesis involves altered histones methylation with gain of global H3K27 methylation, altered Polycomb repressive complex 1 (PRC1) activity, aberrant epigenetic regulation of gene expression and impaired differentiation of mesenchimal progenitor cells. {ECO:0000269|PubMed:27174990}.; ","FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.; ",{"$nulls":4},"p.Lys28Asn","c.84G>C","MODERATE","28/136",1,{"$nulls":5},"5","521","465","394","374","451","401","0.0019","0.0019","0","0.1247",{"$nulls":20},"2.815183",null,null,"0.551555",{"$nulls":3},"0.624",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","510,1","0.002","511","0/1","403,58","0.1258","461",null,"chr6:26045494:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1283"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","HIST1H3C","chr6:26045494","HIST1H3C(K28N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glioma (GLM) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269|PubMed:22286216}. Note=The gene represented in this entry is involved in disease pathogenesis. HIST1H3B mutations affecting residue Lys-28 involved in post-translational modifications of histone H3.1 are recurrent in malignant, aggressive gliomas including pediatric non-brain stem glioblastoma and diffuse intrinsic pontine glioma (DIPG) (PubMed:22286216). The mechanism through which mutations lead to tumorigenesis involves altered histone methylation, impaired regulation of Polycomb repressive complex 2 (PRC2) activity, and aberrant epigenetic regulation of gene expression (PubMed:23603901). {ECO:0000269|PubMed:22286216, ECO:0000269|PubMed:23603901}.; DISEASE: Note=HIST1H3B or HIST1H3C mutations affecting residue Lys-37 of histone H3.1 are involved in the pathogenesis of pediatric undifferentiated soft tissue sarcomas. The mechanism through which mutations lead to tumorigenesis involves altered histones methylation with gain of global H3K27 methylation, altered Polycomb repressive complex 1 (PRC1) activity, aberrant epigenetic regulation of gene expression and impaired differentiation of mesenchimal progenitor cells. {ECO:0000269|PubMed:27174990}.; ","FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.; ",{"$nulls":4},"p.Lys28Asn","c.84G>C","MODERATE","28/136",1,{"$nulls":5},"4","521","563","394","450",null,null,"0.0019","0.0019",{"$nulls":22},"2.815183",null,null,"0.551555",{"$nulls":3},"0.624",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","513,1","0.0019","514","0/1","523,28","0.0508","551",null,"chr6:26045494:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0556"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HLA-B","chr6:31356747","HLA-B(YKAQA91FKTNK)",null,null,"topological domain (Extracellular ), region of interest (Alpha-1 ), sequence variant (In allele B*14:01, allele B*27:01, allele B*27:05, allele B*38:01 and allele B*73:01. HLA-B(Y91C)), sequence variant (In allele B*08:01, allele B*35:01, allele B*51:01, allele B*53:01, allele B*59:01 and allele B*78:01. HLA-B(Y91F)), sequence variant (In allele B*57:01 and allele B*58:01; requires 2 nucleotide substitutions. HLA-B(Y91M)), sequence variant (In allele B*13:02, allele B*15:01, allele B*18:01, allele B*37:01, allele B*39:02, allele B*40:01, allele B*40:02, allele B*41:01, allele B*44:02, allele B*45:01, allele B*47:01, allele B*48:01, allele B*49:01, allele B*50:01 and allele B*52:01. HLA-B(Y91S)), helix ",{"$nulls":3},125,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the presentation of foreign antigens to the immune system.; ",{"$nulls":4},"p.TyrLysAlaGlnAla91PheLysThrAsnLys","c.272_284delACAAGGCCCAGGCinsTCAAGACCAACAA","MODERATE","91/362",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,"AD","Drug-induced toxicity, susceptibility to","General",{"$nulls":3},"C3277286| C1862852| CN160494| C1840547| C1840548| CN077964","0/0","34,0","0","34","0/1","37,11","0.2292","48",null,"chr6:31356747:GCCTGGGCCTTGT:TTGTTGGTCTTGA",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2292"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HLF","chr17:55265596","HLF(D38H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving HLF is a cause of pre-B-cell acute lymphoblastic leukemia (B-ALL). Translocation t(17;19)(q22;p13.3) with TCF3.; ",null,"gedi|level2",{"$nulls":3},"p.Asp38His","c.112G>C","MODERATE","38/295",1,{"$nulls":5},"5","210","228","135","142","190","199","0","0","0","0.1658",{"$nulls":20},"3.821067",null,"0.895","0.999987","-2.14","0.697","0.023","0.205",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC","This gene encodes a member of the proline and acidic-rich (PAR) protein family, a subset of the bZIP transcription factors. The encoded protein forms homodimers or heterodimers with other PAR family members and binds sequence-specific promoter elements to activate transcription. Chromosomal translocations fusing portions of this gene with the E2A gene cause a subset of childhood B-lineage acute lymphoid leukemias. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","202,0","0","202","0/1","177,46","0.2063","223",null,"chr17:55265596:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1831"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HNF4G","chr8:75553139","HNF4G(V186D)",null,null,"domain (NR LBD ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor. Has a lower transcription activation potential than HNF4-alpha.; ",{"$nulls":4},"p.Val186Asp","c.557T>A","MODERATE","186/445",5,{"$nulls":5},"5","277","745","184","496","254","682","0","0","0","0.1408",{"$nulls":20},"4.076277","-4.09","2.81;.","1","-5.24;-5.27","0.992;.","0.0;0.001","0.911",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","255,0","0","255","0/1","625,98","0.1355","723",null,"chr8:75553139:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1351"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HORMAD1","chr1:150704279","HORMAD1(E290G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a key role in meiotic progression. Regulates 3 different functions during meiosis: ensures that sufficient numbers of processed DNA double-strand breaks (DSBs) are available for successful homology search by increasing the steady-state numbers of single-stranded DSB ends. Promotes synaptonemal-complex formation independently of its role in homology search. Plays a key role in the male mid-pachytene checkpoint and the female meiotic prophase checkpoint: required for efficient build-up of ATR activity on unsynapsed chromosome regions, a process believed to form the basis of meiotic silencing of unsynapsed chromatin (MSUC) and meiotic prophase quality control in both sexes. {ECO:0000250|UniProtKB:Q9D5T7}.; ",{"$nulls":4},"p.Glu290Gly","c.869A>G","MODERATE","290/394",11,{"$nulls":5},"1",{"$nulls":30},"0.750004","0.89;1.48;1.49",".;.;-1.065","0.996891;0.998126;0.998126;0.998126","-0.51;-0.61;-0.41","0.0","0.332;0.297;0.31","0.087;0.058;0.057",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","127,0","0","134","0/1","63,4","0.0597","70",null,"chr1:150704279:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HRH4","chr18:24477048","HRH4(S220C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: The H4 subclass of histamine receptors could mediate the histamine signals in peripheral tissues. Displays a significant level of constitutive activity (spontaneous activity in the absence of agonist). {ECO:0000269|PubMed:12503632}.; ",{"$nulls":4},"p.Ser220Cys","c.659C>G","MODERATE","220/390",3,{"$nulls":5},"4","482","481","372","385","431","430","0","0","0","0.2442",{"$nulls":20},"2.611425","-0.57;-0.46","2.48;.","1","-2.38;-2.55","0.992;.","0.028;0.035","0.161;0.393",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","476,0","0","476","0/1","350,123","0.26","473",null,"chr18:24477048:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2545"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","HRH4","chr18:24477048","HRH4(S220C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: The H4 subclass of histamine receptors could mediate the histamine signals in peripheral tissues. Displays a significant level of constitutive activity (spontaneous activity in the absence of agonist). {ECO:0000269|PubMed:12503632}.; ",{"$nulls":4},"p.Ser220Cys","c.659C>G","MODERATE","220/390",3,{"$nulls":5},"4","482","609","372","461","432","543","0","0","0","0.1492",{"$nulls":20},"2.611425","-0.57;-0.46","2.48;.","1","-2.38;-2.55","0.992;.","0.028;0.035","0.161;0.393",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","475,0","0","475","0/1","518,83","0.1381","601",null,"chr18:24477048:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1323"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HSD3B7","chr16:30988092","HSD3B7(R340H)",{"$nulls":6},255,"PASS","Missense","rs745915447",1.537E-5,"DISEASE: Congenital bile acid synthesis defect 1 (CBAS1) [MIM:607765]: A primary defect in bile synthesis leading to progressive liver disease. Clinical features include neonatal jaundice, severe intrahepatic cholestasis, cirrhosis. {ECO:0000269|PubMed:11067870, ECO:0000269|PubMed:12679481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The 3-beta-HSD enzymatic system plays a crucial role in the biosynthesis of all classes of hormonal steroids. HSD VII is active against four 7-alpha-hydroxylated sterols. Does not metabolize several different C(19/21) steroids as substrates. Involved in bile acid synthesis (PubMed:11067870). Plays a key role in cell positioning and movement in lymphoid tissues by mediating degradation of 7-alpha,25-dihydroxycholesterol (7- alpha,25-OHC): 7-alpha,25-OHC acts as a ligand for the G protein- coupled receptor GPR183/EBI2, a chemotactic receptor for a number of lymphoid cells. {ECO:0000250|UniProtKB:Q9EQC1, ECO:0000269|PubMed:11067870}.; ",{"$nulls":4},"p.Arg340His","c.1019G>A","MODERATE","340/369",7,{"$nulls":5},"4","456","499","348","368","397","423","0","0","0","0.1513",{"$nulls":20},"4.041976","-0.16","3.145","0.994913;1;1","-3.05","0.999","0.067","0.447",{"$nulls":3},"ExAC_NFE_AF",1.537E-5,"AR","Bile acid synthesis defect, congenital, 1","Gastrointestinal",{"$nulls":3},"C1843116","0/0","446,0","0","446","0/1","418,71","0.1452","489",null,"chr16:30988092:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1495"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","HSD3B7","chr16:30988092","HSD3B7(R340H)",{"$nulls":6},255,"PASS","Missense","rs745915447",1.537E-5,"DISEASE: Congenital bile acid synthesis defect 1 (CBAS1) [MIM:607765]: A primary defect in bile synthesis leading to progressive liver disease. Clinical features include neonatal jaundice, severe intrahepatic cholestasis, cirrhosis. {ECO:0000269|PubMed:11067870, ECO:0000269|PubMed:12679481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The 3-beta-HSD enzymatic system plays a crucial role in the biosynthesis of all classes of hormonal steroids. HSD VII is active against four 7-alpha-hydroxylated sterols. Does not metabolize several different C(19/21) steroids as substrates. Involved in bile acid synthesis (PubMed:11067870). Plays a key role in cell positioning and movement in lymphoid tissues by mediating degradation of 7-alpha,25-dihydroxycholesterol (7- alpha,25-OHC): 7-alpha,25-OHC acts as a ligand for the G protein- coupled receptor GPR183/EBI2, a chemotactic receptor for a number of lymphoid cells. {ECO:0000250|UniProtKB:Q9EQC1, ECO:0000269|PubMed:11067870}.; ",{"$nulls":4},"p.Arg340His","c.1019G>A","MODERATE","340/369",7,{"$nulls":5},"4","456","564","348","417","396","497","0","0","0","0.0805",{"$nulls":20},"4.041976","-0.16","3.145","0.994913;1;1","-3.05","0.999","0.067","0.447",{"$nulls":3},"ExAC_NFE_AF",1.537E-5,"AR","Bile acid synthesis defect, congenital, 1","Gastrointestinal",{"$nulls":3},"C1843116","0/0","429,0","0","429","0/1","496,39","0.0729","535",null,"chr16:30988092:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0719"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","HTRA3","chr4:8286724","HTRA3(A217P)",null,null,"region of interest (Serine protease ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine protease that cleaves beta-casein/CSN2 as well as several extracellular matrix (ECM) proteoglycans such as decorin/DCN, biglycan/BGN and fibronectin/FN1. Inhibits signaling mediated by TGF-beta family proteins possibly indirectly by degradation of these ECM proteoglycans (By similarity). May act as a tumor suppressor. Negatively regulates, in vitro, trophoblast invasion during placental development and may be involved in the development of the placenta in vivo. May also have a role in ovarian development, granulosa cell differentiation and luteinization (PubMed:21321049, PubMed:22229724). {ECO:0000250|UniProtKB:Q9D236, ECO:0000269|PubMed:21321049, ECO:0000269|PubMed:22229724}.; ",{"$nulls":4},"p.Ala217Pro","c.649G>C","MODERATE","217/453",3,{"$nulls":5},"5","500","638","350","436","474","586","0","0","0","0.2116",{"$nulls":20},"4.232928","-2.87","3.105","1","-4.39;-4.54","0.996;0.984","0.002;0.003","0.978;0.981",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","492,0","0","492","0/1","485,129","0.2101","614",null,"chr4:8286724:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2202"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","HTRA3","chr4:8286724","HTRA3(A217P)",null,null,"region of interest (Serine protease ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine protease that cleaves beta-casein/CSN2 as well as several extracellular matrix (ECM) proteoglycans such as decorin/DCN, biglycan/BGN and fibronectin/FN1. Inhibits signaling mediated by TGF-beta family proteins possibly indirectly by degradation of these ECM proteoglycans (By similarity). May act as a tumor suppressor. Negatively regulates, in vitro, trophoblast invasion during placental development and may be involved in the development of the placenta in vivo. May also have a role in ovarian development, granulosa cell differentiation and luteinization (PubMed:21321049, PubMed:22229724). {ECO:0000250|UniProtKB:Q9D236, ECO:0000269|PubMed:21321049, ECO:0000269|PubMed:22229724}.; ",{"$nulls":4},"p.Ala217Pro","c.649G>C","MODERATE","217/453",3,{"$nulls":5},"5","500","612","350","414","474","563","0","0","0","0.0853",{"$nulls":20},"4.232928","-2.87","3.105","1","-4.39;-4.54","0.996;0.984","0.002;0.003","0.978;0.981",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","490,0","0","490","0/1","526,56","0.0962","582",null,"chr4:8286724:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.087"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","IFNA1","chr9:21441040","IFNA1(S178*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Produced by macrophages, IFN-alpha have antiviral activities. Interferon stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase. {ECO:0000269|PubMed:1634550}.; ","level2",{"$nulls":3},"p.Ser178*","c.533C>G","HIGH","178/189",1,{"$nulls":5},"4","742","633","571","493","918","244","0","0","0","0.4795",{"$nulls":20},"4.614158",null,null,"0.777011",{"$nulls":3},"0.49",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kJAK_STAT,kREGULATION_OF_AUTOPHAGY","The protein encoded by this gene is produced by macrophages and has antiviral activity. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Sep 2011].  ",null,null,"0/0","733,0","0","733","0/1","392,225","0.3647","617",null,"chr9:21441040:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3509"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","IFNA1","chr9:21441040","IFNA1(S178*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Produced by macrophages, IFN-alpha have antiviral activities. Interferon stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase. {ECO:0000269|PubMed:1634550}.; ","level2",{"$nulls":3},"p.Ser178*","c.533C>G","HIGH","178/189",1,{"$nulls":5},"4","742","792","571","610","919","277","0","0","0","0.1913",{"$nulls":20},"4.614158",null,null,"0.777011",{"$nulls":3},"0.49",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kJAK_STAT,kREGULATION_OF_AUTOPHAGY","The protein encoded by this gene is produced by macrophages and has antiviral activity. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Sep 2011].  ",null,null,"0/0","733,0","0","733","0/1","657,135","0.1705","792",null,"chr9:21441040:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1607"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","IFNA10","chr9:21207045","IFNA10(S18F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Produced by macrophages, IFN-alpha have antiviral activities. Interferon stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase.; ","level2",{"$nulls":3},"p.Ser18Phe","c.53C>T","MODERATE","18/189",1,{"$nulls":5},"4","921","929","697","689","888","124","0","0","0","0.2339",{"$nulls":20},"1.6086390000000002","3.98","3.585","1","-3.56","0.957","0.001","0.143",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kJAK_STAT,kREGULATION_OF_AUTOPHAGY","This gene encodes a protein that belongs to the type I interferon family of proteins, and is located in a cluster of alpha interferon genes on chromosome 9. Interferons are small regulatory molecules that function in cell signaling in response to viruses and other pathogens or tumor cells. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Aug 2013].  ",null,null,"0/0","859,0","0","859","0/1","716,180","0.2009","896",null,"chr9:21207045:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1988"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","IL17F","chr6:52238929","IL17F(I19V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Ligand for IL17RA and IL17RC (PubMed:17911633). The heterodimer formed by IL17A and IL17F is a ligand for the heterodimeric complex formed by IL17RA and IL17RC (PubMed:18684971). Involved in stimulating the production of other cytokines such as IL6, IL8 and CSF2, and in regulation of cartilage matrix turnover (PubMed:11591732, PubMed:11591768, PubMed:11574464). Also involved in stimulating the proliferation of peripheral blood mononuclear cells and T-cells and in inhibition of angiogenesis (PubMed:11591732). Plays a role in the induction of neutrophilia in the lungs and in the exacerbation of antigen-induced pulmonary allergic inflammation (By similarity). {ECO:0000250|UniProtKB:Q7TNI7, ECO:0000269|PubMed:11574464, ECO:0000269|PubMed:11591732, ECO:0000269|PubMed:11591768, ECO:0000269|PubMed:17911633, ECO:0000269|PubMed:18684971}.; ",{"$nulls":4},"p.Ile19Val","c.55A>G","MODERATE","19/163",2,{"$nulls":5},"4","252","264","196","209","210","233","0","0","0","0.1631",{"$nulls":20},"0.057956","0.93","0.455","1","-0.08","0.005","0.408","0.076",{"$nulls":3},"Unknown",-1,"AD","Candidiasis, familial, 6","Allergy/Immunology/Infectious",{"$nulls":3},"C3151405","0/0","245,0","0","245","0/1","221,39","0.15","260",null,"chr6:52238929:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1531"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","IL17F","chr6:52238929","IL17F(I19V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Ligand for IL17RA and IL17RC (PubMed:17911633). The heterodimer formed by IL17A and IL17F is a ligand for the heterodimeric complex formed by IL17RA and IL17RC (PubMed:18684971). Involved in stimulating the production of other cytokines such as IL6, IL8 and CSF2, and in regulation of cartilage matrix turnover (PubMed:11591732, PubMed:11591768, PubMed:11574464). Also involved in stimulating the proliferation of peripheral blood mononuclear cells and T-cells and in inhibition of angiogenesis (PubMed:11591732). Plays a role in the induction of neutrophilia in the lungs and in the exacerbation of antigen-induced pulmonary allergic inflammation (By similarity). {ECO:0000250|UniProtKB:Q7TNI7, ECO:0000269|PubMed:11574464, ECO:0000269|PubMed:11591732, ECO:0000269|PubMed:11591768, ECO:0000269|PubMed:17911633, ECO:0000269|PubMed:18684971}.; ",{"$nulls":4},"p.Ile19Val","c.55A>G","MODERATE","19/163",2,{"$nulls":5},"3","252","308","196","239",null,null,"0","0",{"$nulls":22},"0.057956","0.93","0.455","1","-0.08","0.005","0.408","0.076",{"$nulls":3},"Unknown",-1,"AD","Candidiasis, familial, 6","Allergy/Immunology/Infectious",{"$nulls":3},"C3151405","0/0","245,0","0","245","0/1","287,16","0.0528","303",null,"chr6:52238929:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0544"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","IL31RA","chr5:55890096","IL31RA(D245N)",null,null,"topological domain (Extracellular ), domain (Fibronectin type-III 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Amyloidosis, primary localized cutaneous, 2 (PLCA2) [MIM:613955]: A primary amyloidosis characterized by localized cutaneous amyloid deposition. This condition usually presents with itching (especially on the lower legs) and visible changes of skin hyperpigmentation and thickening that may be exacerbated by chronic scratching and rubbing. Primary localized cutaneous amyloidosis is often divided into macular and lichen subtypes although many affected individuals often show both variants coexisting. Lichen amyloidosis characteristically presents as a pruritic eruption of grouped hyperkeratotic papules with a predilection for the shins, calves, ankles and dorsa of feet and thighs. Papules may coalesce to form hyperkeratotic plaques that can resemble lichen planus, lichen simplex or nodular prurigo. Macular amyloidosis is characterized by small pigmented macules that may merge to produce macular hyperpigmentation, sometimes with a reticulate or rippled pattern. In macular and lichen amyloidosis, amyloid is deposited in the papillary dermis in association with grouped colloid bodies, thought to represent degenerate basal keratinocytes. The amyloid deposits probably reflect a combination of degenerate keratin filaments, serum amyloid P component, and deposition of immunoglobulins. {ECO:0000269|PubMed:19690585}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Associates with OSMR to form the interleukin-31 receptor which activates STAT3 and to a lower extent STAT1 and STAT5 (PubMed:11877449, PubMed:14504285, PubMed:15627637, PubMed:15194700). May function in skin immunity (PubMed:15184896). Mediates IL31-induced itch, probably in a manner dependent on cation channels TRPA1 and TRPV1 (By similarity). Positively regulates numbers and cycling status of immature subsets of myeloid progenitor cells in bone marrow in vivo and enhances myeloid progenitor cell survival in vitro (By similarity). {ECO:0000250|UniProtKB:Q8K5B1, ECO:0000269|PubMed:11877449, ECO:0000269|PubMed:14504285, ECO:0000269|PubMed:15184896, ECO:0000269|PubMed:15194700, ECO:0000269|PubMed:15627637}.; ",{"$nulls":4},"p.Asp245Asn","c.733G>A","MODERATE","245/764",6,{"$nulls":5},"4","145","103","102","70","142","97","0","0","0","0.2784",{"$nulls":20},"2.008182","0.5;0.5;0.5;0.5;0.5;.;0.5;.",null,"0.999987","-2.14;-1.87;-1.94;-1.87;-1.87;.;-2.22;.","0.049;0.019;0.008;0.041;0.019;.;.;.","0.112;0.135;0.177;0.159;0.135;.;0.176;.","0.1;0.092;0.09;0.089;0.093;0.092;0.082;0.104",{"$nulls":3},"Unknown",-1,"AD","Amyloidois, primary localized cutaneous, 2","Dermatologic",{"$nulls":3},"C3151404","0/0","142,0","0","142","0/1","74,30","0.2885","104",null,"chr5:55890096:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3143"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","IL31RA","chr5:55890096","IL31RA(D245N)",null,null,"topological domain (Extracellular ), domain (Fibronectin type-III 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Amyloidosis, primary localized cutaneous, 2 (PLCA2) [MIM:613955]: A primary amyloidosis characterized by localized cutaneous amyloid deposition. This condition usually presents with itching (especially on the lower legs) and visible changes of skin hyperpigmentation and thickening that may be exacerbated by chronic scratching and rubbing. Primary localized cutaneous amyloidosis is often divided into macular and lichen subtypes although many affected individuals often show both variants coexisting. Lichen amyloidosis characteristically presents as a pruritic eruption of grouped hyperkeratotic papules with a predilection for the shins, calves, ankles and dorsa of feet and thighs. Papules may coalesce to form hyperkeratotic plaques that can resemble lichen planus, lichen simplex or nodular prurigo. Macular amyloidosis is characterized by small pigmented macules that may merge to produce macular hyperpigmentation, sometimes with a reticulate or rippled pattern. In macular and lichen amyloidosis, amyloid is deposited in the papillary dermis in association with grouped colloid bodies, thought to represent degenerate basal keratinocytes. The amyloid deposits probably reflect a combination of degenerate keratin filaments, serum amyloid P component, and deposition of immunoglobulins. {ECO:0000269|PubMed:19690585}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Associates with OSMR to form the interleukin-31 receptor which activates STAT3 and to a lower extent STAT1 and STAT5 (PubMed:11877449, PubMed:14504285, PubMed:15627637, PubMed:15194700). May function in skin immunity (PubMed:15184896). Mediates IL31-induced itch, probably in a manner dependent on cation channels TRPA1 and TRPV1 (By similarity). Positively regulates numbers and cycling status of immature subsets of myeloid progenitor cells in bone marrow in vivo and enhances myeloid progenitor cell survival in vitro (By similarity). {ECO:0000250|UniProtKB:Q8K5B1, ECO:0000269|PubMed:11877449, ECO:0000269|PubMed:14504285, ECO:0000269|PubMed:15184896, ECO:0000269|PubMed:15194700, ECO:0000269|PubMed:15627637}.; ",{"$nulls":4},"p.Asp245Asn","c.733G>A","MODERATE","245/764",6,{"$nulls":5},"4","145","163","102","110","142","148","0","0","0","0.1216",{"$nulls":20},"2.008182","0.5;0.5;0.5;0.5;0.5;.;0.5;.",null,"0.999987","-2.14;-1.87;-1.94;-1.87;-1.87;.;-2.22;.","0.049;0.019;0.008;0.041;0.019;.;.;.","0.112;0.135;0.177;0.159;0.135;.;0.176;.","0.1;0.092;0.09;0.089;0.093;0.092;0.082;0.104",{"$nulls":3},"Unknown",-1,"AD","Amyloidois, primary localized cutaneous, 2","Dermatologic",{"$nulls":3},"C3151404","0/0","142,0","0","142","0/1","136,25","0.1553","161",null,"chr5:55890096:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1364"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","IL6","chr7:22731520","IL6(R196G)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Rheumatoid arthritis systemic juvenile (RASJ) [MIM:604302]: An inflammatory articular disorder with systemic- onset beginning before the age of 16. It represents a subgroup of juvenile arthritis associated with severe extraarticular features and occasionally fatal complications. During active phases of the disorder, patients display a typical daily spiking fever, an evanescent macular rash, lymphadenopathy, hepatosplenomegaly, serositis, myalgia and arthritis. {ECO:0000269|PubMed:9769329}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Note=A IL6 promoter polymorphism is associated with a lifetime risk of development of Kaposi sarcoma in HIV-infected men. {ECO:0000269|PubMed:11001912}.; ","FUNCTION: Cytokine with a wide variety of biological functions. It is a potent inducer of the acute phase response. Plays an essential role in the final differentiation of B-cells into Ig- secreting cells Involved in lymphocyte and monocyte differentiation. Acts on B-cells, T-cells, hepatocytes, hematopoietic progenitor cells and cells of the CNS. Required for the generation of T(H)17 cells. Also acts as a myokine. It is discharged into the bloodstream after muscle contraction and acts to increase the breakdown of fats and to improve insulin resistance. It induces myeloma and plasmacytoma growth and induces nerve cells differentiation.; ","level2",{"$nulls":3},"p.Arg196Gly","c.586C>G","MODERATE","196/212",5,{"$nulls":5},"5","363","494","261","339","319","438","0","0","0","0.1279",{"$nulls":20},"2.092209","2.11","1.82;1.82;.;.","1","-3.6;-3.6;-3.7;-3.84","1.0;1.0;.;.","0.013;0.013;0.003;0.004","0.429;0.428;0.429;0.465",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kJAK_STAT",null,null,"C0678202| C3538945| C1858558| C0011854| C0917804","0/0","352,0","0","352","0/1","415,62","0.13","477",null,"chr7:22731520:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1268"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","INO80","chr15:41087572","INO80(K216N)",null,null,"region of interest (Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D ), region of interest (Assembles INO80 complex module consisting of conserved components ACTR8, ACTL6A and YY1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: ATPase component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and DNA repair (PubMed:16230350, PubMed:16298340, PubMed:17721549, PubMed:20855601, PubMed:20237820). Binds DNA (PubMed:16298340, PubMed:21303910). As part of the INO80 complex, remodels chromatin by shifting nucleosomes (PubMed:16230350, PubMed:21303910). Regulates transcription upon recruitment by YY1 to YY1-activated genes, where it acts as an essential coactivator (PubMed:17721549). Involved in UV-damage excision DNA repair (PubMed:20855601). The contribution to DNA double-strand break repair appears to be largely indirect through transcriptional regulation (PubMed:20687897). Involved in DNA replication (PubMed:20237820). Required for microtubule assembly during mitosis thereby regulating chromosome segregation cycle (PubMed:20237820). {ECO:0000269|PubMed:16230350, ECO:0000269|PubMed:16298340, ECO:0000269|PubMed:17721549, ECO:0000269|PubMed:20237820, ECO:0000269|PubMed:20687897, ECO:0000269|PubMed:20855601, ECO:0000269|PubMed:21303910}.; ",{"$nulls":4},"p.Lys216Asn","c.648G>C","MODERATE","216/1556",6,{"$nulls":5},"5","422","276","343","223","327","201","0","0","0","0.2488",{"$nulls":20},"3.586593",".;-2.96;-2.96","0.975","0.999989",".;-2.02;-2.02","0.991",".;0.02;0.02",".;0.546;0.523",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a subunit of the chromatin remodeling complex, which is classified into subfamilies depending on sequence features apart from the conserved ATPase domain. This protein is the catalytic ATPase subunit of the INO80 chromatin remodeling complex, which is characterized by a DNA-binding domain. This protein is proposed to bind DNA and be recruited by the YY1 transcription factor to activate certain genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013].",null,null,"0/0","423,0","0","423","0/1","218,55","0.2015","273",null,"chr15:41087572:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1973"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","IRF4","chr6:401627","IRF4(L317F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:9326949}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving IRF4 has been found in multiple myeloma. Translocation t(6;14)(p25;q32) with the IgH locus.; ","FUNCTION: Transcriptional activator. Binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter. Binds the immunoglobulin lambda light chain enhancer, together with PU.1. Probably plays a role in ISRE-targeted signal transduction mechanisms specific to lymphoid cells. Involved in CD8(+) dendritic cell differentiation by forming a complex with the BATF-JUNB heterodimer in immune cells, leading to recognition of AICE sequence (5'-TGAnTCA/GAAA-3'), an immune-specific regulatory element, followed by cooperative binding of BATF and IRF4 and activation of genes (By similarity). {ECO:0000250|UniProtKB:Q64287}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Leu317Phe","c.949C>T","MODERATE","317/451",7,{"$nulls":5},"4","552","738","426","540","496","667","0","0","0","0.1259",{"$nulls":20},"3.859018","-4.09","2.98","1","-3.71","1.0","0.003","0.84",{"$nulls":3},"Unknown",-1,"AD","Skin/hair/eye pigmentation, variation in, 8","Dermatologic","COSMIC",null,null,"C2673265","0/0","535,0","0","535","0/1","608,93","0.1327","701",null,"chr6:401627:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1426"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","IRF4","chr6:401627","IRF4(L317F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:9326949}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving IRF4 has been found in multiple myeloma. Translocation t(6;14)(p25;q32) with the IgH locus.; ","FUNCTION: Transcriptional activator. Binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter. Binds the immunoglobulin lambda light chain enhancer, together with PU.1. Probably plays a role in ISRE-targeted signal transduction mechanisms specific to lymphoid cells. Involved in CD8(+) dendritic cell differentiation by forming a complex with the BATF-JUNB heterodimer in immune cells, leading to recognition of AICE sequence (5'-TGAnTCA/GAAA-3'), an immune-specific regulatory element, followed by cooperative binding of BATF and IRF4 and activation of genes (By similarity). {ECO:0000250|UniProtKB:Q64287}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Leu317Phe","c.949C>T","MODERATE","317/451",7,{"$nulls":5},"4","552","663","426","494","498","605","0","0","0","0.0562",{"$nulls":20},"3.859018","-4.09","2.98","1","-3.71","1.0","0.003","0.84",{"$nulls":3},"Unknown",-1,"AD","Skin/hair/eye pigmentation, variation in, 8","Dermatologic","COSMIC",null,null,"C2673265","0/0","547,0","0","547","0/1","610,38","0.0586","648",null,"chr6:401627:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0567"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ITFG1","chr16:47260615","ITFG1(Y384F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Modulator of T-cell function. Has a protective effect in graft versus host disease model (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Tyr384Phe","c.1151A>T","MODERATE","384/612",11,{"$nulls":5},"5","787","697","540","480","702","605","0","0","0","0.1388",{"$nulls":20},"1.7268240000000001","0.02","0.55;.","0.624467;0.551789","-1.17;-1.14","0.004","0.577;0.549","0.153;0.169",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","753,0","0","753","0/1","573,93","0.1396","666",null,"chr16:47260615:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1396"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ITFG1","chr16:47260615","ITFG1(Y384F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Modulator of T-cell function. Has a protective effect in graft versus host disease model (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Tyr384Phe","c.1151A>T","MODERATE","384/612",11,{"$nulls":5},"5","787","813","540","548","703","733","0","0","0","0.075",{"$nulls":20},"1.7268240000000001","0.02","0.55;.","0.624467;0.551789","-1.17;-1.14","0.004","0.577;0.549","0.153;0.169",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","735,0","0","735","0/1","690,57","0.0763","747",null,"chr16:47260615:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0712"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ITPR3","chr6:33621641","ITPR3(I13M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium.; ",{"$nulls":4},"p.Ile13Met","c.39C>G","MODERATE","13/2671",2,{"$nulls":5},"5","467","395","323","269","406","328","0","0","0","0.1006",{"$nulls":20},"2.984892","-5.06;.","2.375","0.997559","-2.32;.","0.906","0.001;.","0.568",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0011854","0/0","424,0","0","424","0/1","322,33","0.093","355",null,"chr6:33621641:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0892"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ITPR3","chr6:33621641","ITPR3(I13M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium.; ",{"$nulls":4},"p.Ile13Met","c.39C>G","MODERATE","13/2671",2,{"$nulls":5},"5","467","435","323","307","408","362","0","0","0","0.058",{"$nulls":20},"2.984892","-5.06;.","2.375","0.997559","-2.32;.","0.906","0.001;.","0.568",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0011854","0/0","426,0","0","426","0/1","382,24","0.0591","406",null,"chr6:33621641:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0651"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KCMF1","chr2:84971469","KCMF1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Has intrinsic E3 ubiquitin ligase activity and promotes ubiquitination. {ECO:0000269|PubMed:15581609}.; ",{"$nulls":5},"c.16+2T>C","HIGH",null,1,{"$nulls":5},"5","177","187","118","121","157","161","0","0","0","0.0745",{"$nulls":5},"(KCMF1|ENSG00000176407|1|1.00)",{"$nulls":14},"4.063728",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","160,0","0","160","0/1","144,13","0.0828","157",null,"chr2:84971469:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0744"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KCMF1","chr2:84971469","KCMF1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Has intrinsic E3 ubiquitin ligase activity and promotes ubiquitination. {ECO:0000269|PubMed:15581609}.; ",{"$nulls":5},"c.16+2T>C","HIGH",null,1,{"$nulls":5},"5","177","200","118","129","158","174","0","0","0","0.0517",{"$nulls":5},"(KCMF1|ENSG00000176407|1|1.00)",{"$nulls":14},"4.063728",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","147,0","0","147","0/1","151,13","0.0793","164",null,"chr2:84971469:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0698"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KCNMA1","chr10:76877770","KCNMA1(P1279L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Paroxysmal nonkinesigenic dyskinesia, 3, with or without generalized epilepsy (PNKD3) [MIM:609446]: An autosomal dominant neurologic disorder characterized by absence seizures, generalized tonic-clonic seizures, paroxysmal nonkinesigenic dyskinesia and involuntary dystonic or choreiform movements. Onset is usually in childhood. Patients may have seizures only, dyskinesia only, or both. {ECO:0000269|PubMed:15937479, ECO:0000269|PubMed:26195193}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Potassium channel activated by both membrane depolarization or increase in cytosolic Ca(2+) that mediates export of K(+). It is also activated by the concentration of cytosolic Mg(2+). Its activation dampens the excitatory events that elevate the cytosolic Ca(2+) concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity. In smooth muscles, its activation by high level of Ca(2+), caused by ryanodine receptors in the sarcoplasmic reticulum, regulates the membrane potential. In cochlea cells, its number and kinetic properties partly determine the characteristic frequency of each hair cell and thereby helps to establish a tonotopic map. Kinetics of KCNMA1 channels are determined by alternative splicing, phosphorylation status and its combination with modulating beta subunits. Highly sensitive to both iberiotoxin (IbTx) and charybdotoxin (CTX).; ",{"$nulls":4},"p.Pro1279Leu","c.3836C>T","MODERATE","1279/1288",30,{"$nulls":5},"4","558","690","441","541","410","524","0","0","0","0.3435",{"$nulls":20},"2.399416",null,null,"1",{"$nulls":3},".;.;.;.;0.762;.;.;.;.;.;.;.;.;.",{"$nulls":3},"Unknown",-1,"AD","Generalized epilepsy and paroxysmal dyskinesia","Neurologic",{"$nulls":3},"C1836173| C4539985| C5231479| C5231421","0/0","537,0","0","537","0/1","457,220","0.325","677",null,"chr10:76877770:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3087"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KCNMA1","chr10:76877770","KCNMA1(P1279L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Paroxysmal nonkinesigenic dyskinesia, 3, with or without generalized epilepsy (PNKD3) [MIM:609446]: An autosomal dominant neurologic disorder characterized by absence seizures, generalized tonic-clonic seizures, paroxysmal nonkinesigenic dyskinesia and involuntary dystonic or choreiform movements. Onset is usually in childhood. Patients may have seizures only, dyskinesia only, or both. {ECO:0000269|PubMed:15937479, ECO:0000269|PubMed:26195193}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Potassium channel activated by both membrane depolarization or increase in cytosolic Ca(2+) that mediates export of K(+). It is also activated by the concentration of cytosolic Mg(2+). Its activation dampens the excitatory events that elevate the cytosolic Ca(2+) concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity. In smooth muscles, its activation by high level of Ca(2+), caused by ryanodine receptors in the sarcoplasmic reticulum, regulates the membrane potential. In cochlea cells, its number and kinetic properties partly determine the characteristic frequency of each hair cell and thereby helps to establish a tonotopic map. Kinetics of KCNMA1 channels are determined by alternative splicing, phosphorylation status and its combination with modulating beta subunits. Highly sensitive to both iberiotoxin (IbTx) and charybdotoxin (CTX).; ",{"$nulls":4},"p.Pro1279Leu","c.3836C>T","MODERATE","1279/1288",30,{"$nulls":5},"4","558","718","441","561","411","552","0","0","0","0.1214",{"$nulls":20},"2.399416",null,null,"1",{"$nulls":3},".;.;.;.;0.762;.;.;.;.;.;.;.;.;.",{"$nulls":3},"Unknown",-1,"AD","Generalized epilepsy and paroxysmal dyskinesia","Neurologic",{"$nulls":3},"C1836173| C4539985| C5231479| C5231421","0/0","540,0","0","540","0/1","627,78","0.1106","705",null,"chr10:76877770:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1194"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KCNT2","chr1:196258373","KCNT2(R1011Q)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs1388663440",-1,"DISEASE: Epileptic encephalopathy, early infantile, 57 (EIEE57) [MIM:617771]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE57 is an autosomal dominant condition. {ECO:0000269|PubMed:29069600}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Outward rectifying potassium channel. Produces rapidly activating outward rectifier K(+) currents. Activated by high intracellular sodium and chloride levels (PubMed:14684870, PubMed:16687497, PubMed:29069600). Channel activity is inhibited by ATP and by inhalation anesthetics, such as isoflurane (PubMed:16687497) (By similarity). Inhibited upon stimulation of G-protein coupled receptors, such as CHRM1 and GRM1 (PubMed:16687497). {ECO:0000250|UniProtKB:Q6UVM4, ECO:0000269|PubMed:14684870, ECO:0000269|PubMed:16687497, ECO:0000269|PubMed:29069600}.; ",{"$nulls":4},"p.Arg1011Gln","c.3032G>A","MODERATE","1011/1135",26,2,{"$nulls":4},"4","793","1265","559","921","677","1097","0","0","0","0.1012",{"$nulls":20},"4.155593","1.37;.;1.88",".;.;2.375","0.997134;0.997134;0.997134;1","-2.08;.;-1.98","1.0","0.008;.;0.011","0.573;0.563;0.538",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4540411","0/0","754,0","0","754","0/1","1074,121","0.1013","1195",null,"chr1:196258373:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1053"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KCTD2","chr17:75047291","KCTD2(G14A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly14Ala","c.41G>C","MODERATE","14/263",1,{"$nulls":5},"1",{"$nulls":30},"2.198392","-0.0","0.695","0.806722;1","-0.23","0.131","0.54","0.142",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","11,0","0","11","0/1","7,3","0.3","10",null,"chr17:75047291:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KCTD2","chr17:75047291","KCTD2(G14A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly14Ala","c.41G>C","MODERATE","14/263",1,{"$nulls":5},"5","12","28","11","26","11","21","0","0","0","0.1905",{"$nulls":20},"2.198392","-0.0","0.695","0.806722;1","-0.23","0.131","0.54","0.142",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","11,0","0","11","0/1","19,5","0.2083","24",null,"chr17:75047291:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1923"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KDM8","chr16:27213679","KDM8(Q236R)",null,null,"splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone demethylase required for G2/M phase cell cycle progression (PubMed:20457893). Specifically demethylates dimethylated 'Lys-36' (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator (PubMed:20457893). Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation (PubMed:20457893). In a complex with coregulator RCCD1, is also able to demethylate trimethylated 'Lys-36' (H3K36me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with RCCD1 (PubMed:24981860). Possibly together with RCCD1, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha-tubulin acetylation and cytoskeletal microtubule stability (PubMed:28455245). Might function as a protein hydroxylase (PubMed:22851697, PubMed:24100311). Under stress conditions that cause a DNA damage response, acts as a histone protease by cleaving the N-terminal tail of histone H3 at the carboxyl side of monomethyl-lysine (Kme1) residues, preferably at monomethylated 'Lys-9' (H3K9me1) (PubMed:28982940). The histone variant H3F3A is the major target for cleavage (PubMed:28982940). {ECO:0000269|PubMed:20457893, ECO:0000269|PubMed:24981860, ECO:0000269|PubMed:28455245, ECO:0000269|PubMed:28982940, ECO:0000303|PubMed:22851697, ECO:0000303|PubMed:24100311}.; ",{"$nulls":4},"p.Gln236Arg","c.707A>G","MODERATE","236/454",3,{"$nulls":5},"5","492","533","328","357","440","485","0","0","0","0.1031",{"$nulls":20},"1.6961279999999999","2.09","0.27;.","1;1;0.999538;0.999538","-0.33","0.0","0.441;0.255","0.065;0.076",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","458,0","0","458","0/1","450,55","0.1089","505",null,"chr16:27213679:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1092"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KIAA0586","chr14:58467744","KIAA0586(Q808R)",{"$nulls":6},255,"PASS","Missense","rs748872490",6.119e-05,"DISEASE: Joubert syndrome 23 (JBTS23) [MIM:616490]: A mild form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. {ECO:0000269|PubMed:26026149, ECO:0000269|PubMed:26096313, ECO:0000269|PubMed:26386044, ECO:0000269|PubMed:26386247, ECO:0000269|PubMed:26429889}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some patients with biallelic KIAA0586 mutations manifest a disease phenotype with features of Joubert syndrome and additional findings of a small thorax and respiratory problems consistent with Jeune syndrome (Joubert-Jeune ciliopathy). {ECO:0000269|PubMed:26386044}.; DISEASE: Short-rib thoracic dysplasia 14 with polydactyly (SRTD14) [MIM:616546]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:26166481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for ciliogenesis and sonic hedgehog/SHH signaling. Required for the centrosomal recruitment of RAB8A and for the targeting of centriole satellite proteins to centrosomes such as of PCM1. May play a role in early ciliogenesis in the disappearance of centriolar satellites that preceeds ciliary vesicle formation (PubMed:24421332). Involved in regulation of cell intracellular organization. Involved in regulation of cell polarity (By similarity). Required for asymmetrical localization of CEP120 to daughter centrioles (By similarity). {ECO:0000250|UniProtKB:E9PV87, ECO:0000250|UniProtKB:Q1G7G9, ECO:0000269|PubMed:24421332}.; ",{"$nulls":4},"p.Gln808Arg","c.2423A>G","MODERATE","808/1644",18,{"$nulls":5},"4","259","266","198","192","199","208","0","0","0","0.1779",{"$nulls":20},"3.191843","0.31;.;.;.;0.31;0.31",".;.;.;2.395;.;.","0.987073","-1.99;.;.;.;-1.99;-2.15",".;.;.;1.0;.;.","0.128;.;.;.;0.139;0.148","0.58;0.582;0.579;0.576;0.581;0.604",{"$nulls":3},"ExAC_SAS_AF",6.119e-05,{"$nulls":6},"C4084822| C4225286","0/0","252,0","0","252","0/1","218,44","0.1679","262",null,"chr14:58467744:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1667"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KIAA0586","chr14:58467744","KIAA0586(Q808R)",{"$nulls":6},255,"PASS","Missense","rs748872490",6.119e-05,"DISEASE: Joubert syndrome 23 (JBTS23) [MIM:616490]: A mild form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. {ECO:0000269|PubMed:26026149, ECO:0000269|PubMed:26096313, ECO:0000269|PubMed:26386044, ECO:0000269|PubMed:26386247, ECO:0000269|PubMed:26429889}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some patients with biallelic KIAA0586 mutations manifest a disease phenotype with features of Joubert syndrome and additional findings of a small thorax and respiratory problems consistent with Jeune syndrome (Joubert-Jeune ciliopathy). {ECO:0000269|PubMed:26386044}.; DISEASE: Short-rib thoracic dysplasia 14 with polydactyly (SRTD14) [MIM:616546]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:26166481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for ciliogenesis and sonic hedgehog/SHH signaling. Required for the centrosomal recruitment of RAB8A and for the targeting of centriole satellite proteins to centrosomes such as of PCM1. May play a role in early ciliogenesis in the disappearance of centriolar satellites that preceeds ciliary vesicle formation (PubMed:24421332). Involved in regulation of cell intracellular organization. Involved in regulation of cell polarity (By similarity). Required for asymmetrical localization of CEP120 to daughter centrioles (By similarity). {ECO:0000250|UniProtKB:E9PV87, ECO:0000250|UniProtKB:Q1G7G9, ECO:0000269|PubMed:24421332}.; ",{"$nulls":4},"p.Gln808Arg","c.2423A>G","MODERATE","808/1644",18,{"$nulls":5},"4","259","278","198","204","198","220","0","0","0","0.0727",{"$nulls":20},"3.191843","0.31;.;.;.;0.31;0.31",".;.;.;2.395;.;.","0.987073","-1.99;.;.;.;-1.99;-2.15",".;.;.;1.0;.;.","0.128;.;.;.;0.139;0.148","0.58;0.582;0.579;0.576;0.581;0.604",{"$nulls":3},"ExAC_SAS_AF",6.119e-05,{"$nulls":6},"C4084822| C4225286","0/0","252,0","0","252","0/1","250,22","0.0809","272",null,"chr14:58467744:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0784"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KIAA0825","chr5:94464927","KIAA0825(L669V)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu669Val","c.2005C>G","MODERATE","669/1275",10,{"$nulls":5},"5","268","260","204","186","232","225","0","0","0","0.1822",{"$nulls":20},"1.427079","0.89","1.79","0.564721","0.02","0.275","0.45","0.064",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193129","0/0","259,0","0","259","0/1","201,44","0.1796","245",null,"chr5:94464927:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1774"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KIAA0825","chr5:94464927","KIAA0825(L669V)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu669Val","c.2005C>G","MODERATE","669/1275",10,{"$nulls":5},"5","268","293","204","219","231","260","0","0","0","0.0731",{"$nulls":20},"1.427079","0.89","1.79","0.564721","0.02","0.275","0.45","0.064",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193129","0/0","263,0","0","263","0/1","263,23","0.0804","286",null,"chr5:94464927:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0776"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KIAA1429","chr8:94495743","KIAA1429(L1511Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu1511Gln","c.4532T>A","MODERATE","1511/1812",19,{"$nulls":5},"5","236","478","199","410","166","331","0","0","0","0.1057",{"$nulls":20},"2.871681","1.58","0.49","0.906577;1","4.38","0.02","0.132","0.454",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","231,1","0.0043","232","0/1","428,40","0.0855","468",null,"chr8:94495743:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0829"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KIAA1522","chr1:32771167","KIAA1522(H663P)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.His663Pro","c.1988A>C","MODERATE","663/1094",6,{"$nulls":5},"4","247","274",null,null,"214","226","0","0","0","0.0752",{"$nulls":20},"2.19314","2.75;2.75;2.76",".;.;2.045","0.959823;0.959823;0.959823;1","-1.13;-0.95;-0.03","0.106;0.039;0.039","0.0","0.498;0.507;0.575",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","222,0","0","222","0/1","230,20","0.08","250",null,"chr1:32771167:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KRT28","chr17:40799892","KRT28(M1fs)",null,null,"region of interest (Head )","miscellaneous-region:Head","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Essential for the proper assembly of types I and II keratin protein complexes and the formation of keratin intermediate filaments in the inner root sheath (irs). {ECO:0000250|UniProtKB:A6BLY7}.; ",{"$nulls":4},"p.Met1fs","c.-22_1delGGTGAACATTTCTCAAAACACCA","HIGH","1/464",1,{"$nulls":5},"4","149","147","117","102","80","89","0","0","0","0.4382",{"$nulls":5},"(KRT28|ENSG00000173908|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","148,0","0","148","0/1","89,48","0.3504","137",null,"chr17:40799892:ATGGTGTTTTGAGAAATGTTCACC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3333"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KRT28","chr17:40799892","KRT28(M1fs)",null,null,"region of interest (Head )","miscellaneous-region:Head","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Essential for the proper assembly of types I and II keratin protein complexes and the formation of keratin intermediate filaments in the inner root sheath (irs). {ECO:0000250|UniProtKB:A6BLY7}.; ",{"$nulls":4},"p.Met1fs","c.-22_1delGGTGAACATTTCTCAAAACACCA","HIGH","1/464",1,{"$nulls":5},"4","149","131","117","102",null,null,"0","0",{"$nulls":7},"(KRT28|ENSG00000173908|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","148,0","0","148","0/1","114,18","0.1364","132",null,"chr17:40799892:ATGGTGTTTTGAGAAATGTTCACC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1275"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KRTAP19-1","chr21:30480201","KRTAP19-1(C39*)",null,null,"region of interest (26 X 2 AA repeats of G-[YCGS] )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.; ",{"$nulls":4},"p.Cys39*","c.117T>A","HIGH","39/90",1,{"$nulls":5},"4","729","1145","578","913","222","353","0","0","0","0.1558",{"$nulls":20},"4.100686",null,null,"0.78567",{"$nulls":3},"0.071",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","727,2","0.0027","729","0/1","993,144","0.1266","1137",null,"chr21:30480201:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.126"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","KRTAP19-1","chr21:30480201","KRTAP19-1(C39*)",null,null,"region of interest (26 X 2 AA repeats of G-[YCGS] )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated proteins (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.; ",{"$nulls":4},"p.Cys39*","c.117T>A","HIGH","39/90",1,{"$nulls":5},"4","729","858","578","658","221","240","0","0","0","0.0542",{"$nulls":20},"4.100686",null,null,"0.78567",{"$nulls":3},"0.071",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","728,2","0.0027","730","0/1","817,49","0.0566","866",null,"chr21:30480201:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0623"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KRTAP5-10","chr11:71565611","KRTAP5-10(G16_C17insCGSGCGG)",{"$nulls":6},124,"PASS","Inframe Indel","rs71049990",-1,null,"FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.; ",{"$nulls":4},"p.Gly16_Cys17insCysGlySerGlyCysGlyGly","c.27_47dupCTGTGGCTCCGGCTGTGGGGG","MODERATE","16/202",1,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","79,0","0","82","0/1","58,21","0.2308","91",null,"chr11:71565611:A:AGGCTGTGGCTCCGGCTGTGGG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2308"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","KRTAP5-7","chr11:71527629","KRTAP5-7(C132_S133insQSSCCKPCCC)",null,null,"region of interest (7 X 4 AA repeats of C-C-X-P )",{"$nulls":3},291,"PASS","Inframe Indel","rs771895560",-1,null,"FUNCTION: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high- sulfur and high-glycine-tyrosine keratins.; ",{"$nulls":4},"p.Cys132_Ser133insGlnSerSerCysCysLysProCysCysCys","c.366_395dupCCAGTCCAGCTGCTGTAAGCCCTGCTGCTG","MODERATE","132/165",1,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","184,0","0","875","0/1","130,642","0.8515","754",null,"chr11:71527629:C:CCTGCTGCCAGTCCAGCTGCTGTAAGCCCTG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.8515"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LAMB1","chr7:107959735","LAMB1(R829T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Lissencephaly 5 (LIS5) [MIM:615191]: An autosomal recessive brain malformation characterized by cobblestone changes in the cortex, more severe in the posterior region, and subcortical band heterotopia. Affected individuals have hydrocephalus, seizures, and severely delayed psychomotor development. {ECO:0000269|PubMed:23472759}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Involved in the organization of the laminar architecture of cerebral cortex. It is probably required for the integrity of the basement membrane/glia limitans that serves as an anchor point for the endfeet of radial glial cells and as a physical barrier to migrating neurons. Radial glial cells play a central role in cerebral cortical development, where they act both as the proliferative unit of the cerebral cortex and a scaffold for neurons migrating toward the pial surface. {ECO:0000269|PubMed:23472759}.; ","level2",{"$nulls":3},"p.Arg829Thr","c.2486G>C","MODERATE","829/1810",17,{"$nulls":5},"4","814","876","592","643","732","773","0","0","0","0.3157",{"$nulls":20},"2.570164","-0.06",".;2;.","0.956308","-3.62;-3.62;-3.78","0.259;0.372;0.082","0.192;0.243;0.122","0.508;0.509;0.441",{"$nulls":3},"Unknown",-1,"AR","Lissencephaly 5","Neurologic","kCANCER",null,null,"C3554657","0/0","782,0","0","782","0/1","579,262","0.3115","841",null,"chr7:107959735:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2986"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LAMB1","chr7:107959735","LAMB1(R829T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Lissencephaly 5 (LIS5) [MIM:615191]: An autosomal recessive brain malformation characterized by cobblestone changes in the cortex, more severe in the posterior region, and subcortical band heterotopia. Affected individuals have hydrocephalus, seizures, and severely delayed psychomotor development. {ECO:0000269|PubMed:23472759}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Involved in the organization of the laminar architecture of cerebral cortex. It is probably required for the integrity of the basement membrane/glia limitans that serves as an anchor point for the endfeet of radial glial cells and as a physical barrier to migrating neurons. Radial glial cells play a central role in cerebral cortical development, where they act both as the proliferative unit of the cerebral cortex and a scaffold for neurons migrating toward the pial surface. {ECO:0000269|PubMed:23472759}.; ","level2",{"$nulls":3},"p.Arg829Thr","c.2486G>C","MODERATE","829/1810",17,{"$nulls":5},"4","814","1008","592","718","733","880","0","0","0","0.1216",{"$nulls":20},"2.570164","-0.06",".;2;.","0.956308","-3.62;-3.62;-3.78","0.259;0.372;0.082","0.192;0.243;0.122","0.508;0.509;0.441",{"$nulls":3},"Unknown",-1,"AR","Lissencephaly 5","Neurologic","kCANCER",null,null,"C3554657","0/0","756,0","0","756","0/1","827,120","0.1267","947",null,"chr7:107959735:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1267"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LAS1L","chrX:65524076","LAS1L(I427N)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Wilson-Turner X-linked mental retardation syndrome (WTS) [MIM:309585]: A neurologic disorder characterized by severe intellectual disability, dysmorphic facial features, hypogonadism, short stature, and truncal obesity. Affected females have a milder phenotype than affected males. {ECO:0000269|PubMed:25644381}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the biogenesis of the 60S ribosomal subunit. Required for maturation of the 28S rRNA. Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes. {ECO:0000269|PubMed:20647540, ECO:0000269|PubMed:22872859}.; ",{"$nulls":4},"p.Ile427Asn","c.1280T>A","MODERATE","427/734",10,{"$nulls":5},"5","367","353","312","302","293","258","0","0","0","0.1938",{"$nulls":20},"2.80357",null,".;2.635;.","1;0.759966;0.759966;0.759966","-3.37;-3.33;-3.67","0.007;0.001;0.005","0.002","0.766;0.757;0.666",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1839736","0/0","360,0","0","360","0/1","277,60","0.178","337",null,"chrX:65524076:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1821"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LAS1L","chrX:65524076","LAS1L(I427N)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Wilson-Turner X-linked mental retardation syndrome (WTS) [MIM:309585]: A neurologic disorder characterized by severe intellectual disability, dysmorphic facial features, hypogonadism, short stature, and truncal obesity. Affected females have a milder phenotype than affected males. {ECO:0000269|PubMed:25644381}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the biogenesis of the 60S ribosomal subunit. Required for maturation of the 28S rRNA. Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes. {ECO:0000269|PubMed:20647540, ECO:0000269|PubMed:22872859}.; ",{"$nulls":4},"p.Ile427Asn","c.1280T>A","MODERATE","427/734",10,{"$nulls":5},"5","367","412","312","356","294","331","0","0","0","0.1148",{"$nulls":20},"2.80357",null,".;2.635;.","1;0.759966;0.759966;0.759966","-3.37;-3.33;-3.67","0.007;0.001;0.005","0.002","0.766;0.757;0.666",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1839736","0/0","359,0","0","359","0/1","363,39","0.097","402",null,"chrX:65524076:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0983"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LMOD2","chr7:123663090","LMOD2(S502P)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,14.32,"PASS","Missense",null,-1,null,"FUNCTION: Mediates nucleation of actin filaments and thereby promotes actin polymerization (PubMed:18403713, PubMed:26370058, PubMed:25250574, PubMed:26417072). Plays a role in the regulation of actin filament length (By similarity). Required for normal sarcomere organization in the heart, and for normal heart function (PubMed:18403713). {ECO:0000250|UniProtKB:Q3UHZ5, ECO:0000269|PubMed:18403713, ECO:0000269|PubMed:25250574, ECO:0000269|PubMed:26370058, ECO:0000269|PubMed:26417072}.; ",{"$nulls":4},"p.Ser502Pro","c.1504T>C","MODERATE","502/547",2,{"$nulls":5},"1",{"$nulls":30},"1.853418","1.25","-0.04;.","0.784492;0.988195","3.06;-0.62","0.001;.","0.466;0.135","0.205;0.071",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0|0","294,0","0","214","0|1","315,20","0.0597","234",null,"chr7:123663090:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LOXL2","chr8:23368075","LOXL2(A93T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the post-translational oxidative deamination of lysine residues on target proteins leading to the formation of deaminated lysine (allysine) (PubMed:27735137). Acts as a transcription corepressor and specifically mediates deamination of trimethylated 'Lys-4' of histone H3 (H3K4me3), a specific tag for epigenetic transcriptional activation (PubMed:27735137). Shows no activity against histone H3 when it is trimethylated on 'Lys-9' (H3K9me3) or 'Lys-27' (H3K27me3) or when 'Lys-4' is monomethylated (H3K4me1) or dimethylated (H3K4me2) (PubMed:27735137). Also mediates deamination of methylated TAF10, a member of the transcription factor IID (TFIID) complex, which induces release of TAF10 from promoters, leading to inhibition of TFIID-dependent transcription (PubMed:25959397). LOXL2-mediated deamination of TAF10 results in transcriptional repression of genes required for embryonic stem cell pluripotency including POU5F1/OCT4, NANOG, KLF4 and SOX2 (By similarity). Involved in epithelial to mesenchymal transition (EMT) via interaction with SNAI1 and participates in repression of E-cadherin CDH1, probably by mediating deamination of histone H3 (PubMed:16096638, PubMed:27735137, PubMed:24414204). During EMT, involved with SNAI1 in negatively regulating pericentromeric heterochromatin transcription (PubMed:24239292). SNAI1 recruits LOXL2 to pericentromeric regions to oxidize histone H3 and repress transcription which leads to release of heterochromatin component CBX5/HP1A, enabling chromatin reorganization and acquisition of mesenchymal traits (PubMed:24239292). Interacts with the endoplasmic reticulum protein HSPA5 which activates the IRE1-XBP1 pathway of the unfolded protein response, leading to expression of several transcription factors involved in EMT and subsequent EMT induction (PubMed:28332555). Involved in E-cadherin repression following hypoxia, a hallmark of EMT believed to amplify tumor aggressiveness, suggesting that it may play a role in tumor progression (PubMed:20026874). When secreted into the extracellular matrix, promotes cross-linking of extracellular matrix proteins by mediating oxidative deamination of peptidyl lysine residues in precursors to fibrous collagen and elastin (PubMed:20306300). Acts as a regulator of sprouting angiogenesis, probably via collagen IV scaffolding (PubMed:21835952). Acts as a regulator of chondrocyte differentiation, probably by regulating expression of factors that control chondrocyte differentiation (By similarity). {ECO:0000250|UniProtKB:P58022, ECO:0000269|PubMed:16096638, ECO:0000269|PubMed:20026874, ECO:0000269|PubMed:20306300, ECO:0000269|PubMed:21835952, ECO:0000269|PubMed:24239292, ECO:0000269|PubMed:24414204, ECO:0000269|PubMed:25959397, ECO:0000269|PubMed:27735137}.; ",{"$nulls":4},"p.Ala93Thr","c.277G>A","MODERATE","93/774",2,{"$nulls":5},"5","326","223","239","162","295","202","0","0","0","0.2079",{"$nulls":20},"4.061539","0.82;0.82;0.82;0.82;-0.92;-0.92","2.96;.;.;.;.;.","1","-3.2;-3.96;-3.96;-4.0;-4.0;-3.87","0.999;.;.;.;.;.","0.001;0.003;0.004;0.0;0.0;0.0","0.946;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","321,0","0","321","0/1","172,47","0.2146","219",null,"chr8:23368075:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.216"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LOXL2","chr8:23368075","LOXL2(A93T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the post-translational oxidative deamination of lysine residues on target proteins leading to the formation of deaminated lysine (allysine) (PubMed:27735137). Acts as a transcription corepressor and specifically mediates deamination of trimethylated 'Lys-4' of histone H3 (H3K4me3), a specific tag for epigenetic transcriptional activation (PubMed:27735137). Shows no activity against histone H3 when it is trimethylated on 'Lys-9' (H3K9me3) or 'Lys-27' (H3K27me3) or when 'Lys-4' is monomethylated (H3K4me1) or dimethylated (H3K4me2) (PubMed:27735137). Also mediates deamination of methylated TAF10, a member of the transcription factor IID (TFIID) complex, which induces release of TAF10 from promoters, leading to inhibition of TFIID-dependent transcription (PubMed:25959397). LOXL2-mediated deamination of TAF10 results in transcriptional repression of genes required for embryonic stem cell pluripotency including POU5F1/OCT4, NANOG, KLF4 and SOX2 (By similarity). Involved in epithelial to mesenchymal transition (EMT) via interaction with SNAI1 and participates in repression of E-cadherin CDH1, probably by mediating deamination of histone H3 (PubMed:16096638, PubMed:27735137, PubMed:24414204). During EMT, involved with SNAI1 in negatively regulating pericentromeric heterochromatin transcription (PubMed:24239292). SNAI1 recruits LOXL2 to pericentromeric regions to oxidize histone H3 and repress transcription which leads to release of heterochromatin component CBX5/HP1A, enabling chromatin reorganization and acquisition of mesenchymal traits (PubMed:24239292). Interacts with the endoplasmic reticulum protein HSPA5 which activates the IRE1-XBP1 pathway of the unfolded protein response, leading to expression of several transcription factors involved in EMT and subsequent EMT induction (PubMed:28332555). Involved in E-cadherin repression following hypoxia, a hallmark of EMT believed to amplify tumor aggressiveness, suggesting that it may play a role in tumor progression (PubMed:20026874). When secreted into the extracellular matrix, promotes cross-linking of extracellular matrix proteins by mediating oxidative deamination of peptidyl lysine residues in precursors to fibrous collagen and elastin (PubMed:20306300). Acts as a regulator of sprouting angiogenesis, probably via collagen IV scaffolding (PubMed:21835952). Acts as a regulator of chondrocyte differentiation, probably by regulating expression of factors that control chondrocyte differentiation (By similarity). {ECO:0000250|UniProtKB:P58022, ECO:0000269|PubMed:16096638, ECO:0000269|PubMed:20026874, ECO:0000269|PubMed:20306300, ECO:0000269|PubMed:21835952, ECO:0000269|PubMed:24239292, ECO:0000269|PubMed:24414204, ECO:0000269|PubMed:25959397, ECO:0000269|PubMed:27735137}.; ",{"$nulls":4},"p.Ala93Thr","c.277G>A","MODERATE","93/774",2,{"$nulls":5},"5","326","259","239","172","295","238","0","0","0","0.0588",{"$nulls":20},"4.061539","0.82;0.82;0.82;0.82;-0.92;-0.92","2.96;.;.;.;.;.","1","-3.2;-3.96;-3.96;-4.0;-4.0;-3.87","0.999;.;.;.;.;.","0.001;0.003;0.004;0.0;0.0;0.0","0.946;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","321,0","0","321","0/1","240,18","0.0698","258",null,"chr8:23368075:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0814"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRP12","chr8:104491054","LRP12(M733I)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. May act as a tumor suppressor. {ECO:0000269|PubMed:12809483}.; ",{"$nulls":4},"p.Met733Ile","c.2199G>C","MODERATE","733/859",7,{"$nulls":5},"4","619","1754","478","1367","478","1420","0","0","0","0.0662",{"$nulls":20},"2.01303","-1.66;-1.6",".;0.805","0.99998;0.99998;0.999988","-0.02","0.0","0.063;0.061","0.2;0.22",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5231388","0/0","614,0","0","614","0/1","1598,107","0.0628","1705",null,"chr8:104491054:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.06"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRP1B","chr2:140601481","LRP1B(P2320S)",null,null,"topological domain (Extracellular ), repeat (LDL-receptor class B 22 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis.; ","gedi|foundationOne",{"$nulls":3},"p.Pro2320Ser","c.6958C>T","MODERATE","2320/4599",42,{"$nulls":5},"4","449","630","334","468","370","492","0","0","0","0.063",{"$nulls":20},"4.150372","-3.29","3.32","1","-6.92","1.0",null,"0.714",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","425,0","0","425","0/1","561,35","0.0587","596",null,"chr2:140601481:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0598"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRP2","chr2:169206023","LRP2(G2519V)",{"$nulls":3},"repeat:LDL-receptor_class_B_27","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Donnai-Barrow syndrome (DBS) [MIM:222448]: Rare autosomal recessive disorder characterized by major malformations including agenesis of the corpus callosum, congenital diaphragmatic hernia, facial dysmorphology, ocular anomalies, sensorineural hearing loss and developmental delay. The FOAR syndrome was first described as comprising facial anomalies, ocular anomalies, sensorineural hearing loss, and proteinuria. DBS and FOAR were first described as distinct disorders but the classic distinguishing features between the 2 disorders were presence of proteinuria and absence of diaphragmatic hernia and corpus callosum anomalies in FOAR. Early reports noted that the 2 disorders shared many phenotypic features and may be identical. Although there is variability in the expression of some features (e.g., agenesis of the corpus callosum and proteinuria), DBS and FOAR are now considered to represent the same entity. {ECO:0000269|PubMed:17632512}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Multiligand endocytic receptor (By similarity). Acts together with CUBN to mediate endocytosis of high-density lipoproteins (By similarity). Mediates receptor-mediated uptake of polybasic drugs such as aprotinin, aminoglycosides and polymyxin B (By similarity). In the kidney, mediates the tubular uptake and clearance of leptin (By similarity). Also mediates transport of leptin across the blood-brain barrier through endocytosis at the choroid plexus epithelium (By similarity). Endocytosis of leptin in neuronal cells is required for hypothalamic leptin signaling and leptin-mediated regulation of feeding and body weight (By similarity). Mediates endocytosis and subsequent lysosomal degradation of CST3 in kidney proximal tubule cells (By similarity). Mediates renal uptake of 25-hydroxyvitamin D3 in complex with the vitamin D3 transporter GC/DBP (By similarity). Mediates renal uptake of metallothionein-bound heavy metals (PubMed:15126248). Together with CUBN, mediates renal reabsorption of myoglobin (By similarity). Mediates renal uptake and subsequent lysosomal degradation of APOM (By similarity). Plays a role in kidney selenium homeostasis by mediating renal endocytosis of selenoprotein SEPP1 (By similarity). Mediates renal uptake of the antiapoptotic protein BIRC5/survivin which may be important for functional integrity of the kidney (PubMed:23825075). Mediates renal uptake of matrix metalloproteinase MMP2 in complex with metalloproteinase inhibitor TIMP1 (By similarity). Mediates endocytosis of Sonic hedgehog protein N-product (ShhN), the active product of SHH (By similarity). Also mediates ShhN transcytosis (By similarity). In the embryonic neuroepithelium, mediates endocytic uptake and degradation of BMP4, is required for correct SHH localization in the ventral neural tube and plays a role in patterning of the ventral telencephalon (By similarity). Required at the onset of neurulation to sequester SHH on the apical surface of neuroepithelial cells of the rostral diencephalon ventral midline and to control PTCH1-dependent uptake and intracellular trafficking of SHH (By similarity). During neurulation, required in neuroepithelial cells for uptake of folate bound to the folate receptor FOLR1 which is necessary for neural tube closure (By similarity). In the adult brain, negatively regulates BMP signaling in the subependymal zone which enables neurogenesis to proceed (By similarity). In astrocytes, mediates endocytosis of ALB which is required for the synthesis of the neurotrophic factor oleic acid (By similarity). Involved in neurite branching (By similarity). During optic nerve development, required for SHH- mediated migration and proliferation of oligodendrocyte precursor cells (By similarity). Mediates endocytic uptake and clearance of SHH in the retinal margin which protects retinal progenitor cells from mitogenic stimuli and keeps them quiescent (By similarity). Plays a role in reproductive organ development by mediating uptake in reproductive tissues of androgen and estrogen bound to the sex hormone binding protein SHBG (By similarity). Mediates endocytosis of angiotensin-2 (By similarity). Also mediates endocytosis of angiotensis 1-7 (By similarity). Binds to the complex composed of beta-amyloid protein 40 and CLU/APOJ and mediates its endocytosis and lysosomal degradation (By similarity). Required for embryonic heart development (By similarity). Required for normal hearing, possibly through interaction with estrogen in the inner ear (By similarity). {ECO:0000250|UniProtKB:A2ARV4, ECO:0000250|UniProtKB:C0HL13, ECO:0000250|UniProtKB:P98158, ECO:0000269|PubMed:15126248, ECO:0000269|PubMed:23825075}.; ","level2",{"$nulls":3},"p.Gly2519Val","c.7556G>T","MODERATE","2519/4655",40,{"$nulls":5},"4","297","370","255","326","216","284","0.0034","0.0034","0","0.1408",{"$nulls":20},"6.011852",".;-3.5","4.13","1",".;-8.36","1.0",".;0.002",".;0.961",{"$nulls":3},"Unknown",-1,"AR","Donnai-Barrow syndrome; Faciooculoacousticorenal syndrome","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Ophthalmologic; Renal","kHEDGEHOG",null,null,"C1857277","0/0","296,1","0.0034","297","0/1","321,46","0.1253","367",null,"chr2:169206023:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1227"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LRP2","chr2:169206023","LRP2(G2519V)",{"$nulls":3},"repeat:LDL-receptor_class_B_27","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Donnai-Barrow syndrome (DBS) [MIM:222448]: Rare autosomal recessive disorder characterized by major malformations including agenesis of the corpus callosum, congenital diaphragmatic hernia, facial dysmorphology, ocular anomalies, sensorineural hearing loss and developmental delay. The FOAR syndrome was first described as comprising facial anomalies, ocular anomalies, sensorineural hearing loss, and proteinuria. DBS and FOAR were first described as distinct disorders but the classic distinguishing features between the 2 disorders were presence of proteinuria and absence of diaphragmatic hernia and corpus callosum anomalies in FOAR. Early reports noted that the 2 disorders shared many phenotypic features and may be identical. Although there is variability in the expression of some features (e.g., agenesis of the corpus callosum and proteinuria), DBS and FOAR are now considered to represent the same entity. {ECO:0000269|PubMed:17632512}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Multiligand endocytic receptor (By similarity). Acts together with CUBN to mediate endocytosis of high-density lipoproteins (By similarity). Mediates receptor-mediated uptake of polybasic drugs such as aprotinin, aminoglycosides and polymyxin B (By similarity). In the kidney, mediates the tubular uptake and clearance of leptin (By similarity). Also mediates transport of leptin across the blood-brain barrier through endocytosis at the choroid plexus epithelium (By similarity). Endocytosis of leptin in neuronal cells is required for hypothalamic leptin signaling and leptin-mediated regulation of feeding and body weight (By similarity). Mediates endocytosis and subsequent lysosomal degradation of CST3 in kidney proximal tubule cells (By similarity). Mediates renal uptake of 25-hydroxyvitamin D3 in complex with the vitamin D3 transporter GC/DBP (By similarity). Mediates renal uptake of metallothionein-bound heavy metals (PubMed:15126248). Together with CUBN, mediates renal reabsorption of myoglobin (By similarity). Mediates renal uptake and subsequent lysosomal degradation of APOM (By similarity). Plays a role in kidney selenium homeostasis by mediating renal endocytosis of selenoprotein SEPP1 (By similarity). Mediates renal uptake of the antiapoptotic protein BIRC5/survivin which may be important for functional integrity of the kidney (PubMed:23825075). Mediates renal uptake of matrix metalloproteinase MMP2 in complex with metalloproteinase inhibitor TIMP1 (By similarity). Mediates endocytosis of Sonic hedgehog protein N-product (ShhN), the active product of SHH (By similarity). Also mediates ShhN transcytosis (By similarity). In the embryonic neuroepithelium, mediates endocytic uptake and degradation of BMP4, is required for correct SHH localization in the ventral neural tube and plays a role in patterning of the ventral telencephalon (By similarity). Required at the onset of neurulation to sequester SHH on the apical surface of neuroepithelial cells of the rostral diencephalon ventral midline and to control PTCH1-dependent uptake and intracellular trafficking of SHH (By similarity). During neurulation, required in neuroepithelial cells for uptake of folate bound to the folate receptor FOLR1 which is necessary for neural tube closure (By similarity). In the adult brain, negatively regulates BMP signaling in the subependymal zone which enables neurogenesis to proceed (By similarity). In astrocytes, mediates endocytosis of ALB which is required for the synthesis of the neurotrophic factor oleic acid (By similarity). Involved in neurite branching (By similarity). During optic nerve development, required for SHH- mediated migration and proliferation of oligodendrocyte precursor cells (By similarity). Mediates endocytic uptake and clearance of SHH in the retinal margin which protects retinal progenitor cells from mitogenic stimuli and keeps them quiescent (By similarity). Plays a role in reproductive organ development by mediating uptake in reproductive tissues of androgen and estrogen bound to the sex hormone binding protein SHBG (By similarity). Mediates endocytosis of angiotensin-2 (By similarity). Also mediates endocytosis of angiotensis 1-7 (By similarity). Binds to the complex composed of beta-amyloid protein 40 and CLU/APOJ and mediates its endocytosis and lysosomal degradation (By similarity). Required for embryonic heart development (By similarity). Required for normal hearing, possibly through interaction with estrogen in the inner ear (By similarity). {ECO:0000250|UniProtKB:A2ARV4, ECO:0000250|UniProtKB:C0HL13, ECO:0000250|UniProtKB:P98158, ECO:0000269|PubMed:15126248, ECO:0000269|PubMed:23825075}.; ","level2",{"$nulls":3},"p.Gly2519Val","c.7556G>T","MODERATE","2519/4655",40,{"$nulls":5},"4","297","393","255","327","215","306","0.0034","0.0034","0","0.0817",{"$nulls":20},"6.011852",".;-3.5","4.13","1",".;-8.36","1.0",".;0.002",".;0.961",{"$nulls":3},"Unknown",-1,"AR","Donnai-Barrow syndrome; Faciooculoacousticorenal syndrome","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Ophthalmologic; Renal","kHEDGEHOG",null,null,"C1857277","0/0","298,1","0.0033","299","0/1","351,27","0.0714","378",null,"chr2:169206023:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0734"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRRC25","chr19:18396438","LRRC25(V171_L175del)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Plays a role in the inhibition of RLR-mediated type I interferon signaling pathway by targeting DDX58/RIG-I for autophagic degradation. Interacts specifically with ISG15- associated DDX58 to promote interaction between DDX58 and the autophagic cargo receptor p62/SQSTM1 to mediate DDX58 degradation via selective autophagy (PubMed:29288164). Plays also a role in the inhibition of NF-kappa-B signaling pathway and inflammatory response by promoting the degradation of p65/RELA. {ECO:0000269|PubMed:12384430, ECO:0000269|PubMed:29044191, ECO:0000269|PubMed:29288164}.; ",{"$nulls":4},"p.Val171_Leu175del","c.511_525delGTCAGCGGGTGCCTG","MODERATE","171/305",1,{"$nulls":5},"5","287","210","245","172","279","198","0","0","0","0.202",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","337,0","0","337","0/1","194,43","0.1814","237",null,"chr19:18396438:GCAGGCACCCGCTGAC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2093"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRRC47","chr1:3781561","LRRC47(S485T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser485Thr","c.1454G>C","MODERATE","485/583",6,{"$nulls":5},"5","161","89","119","57","146","78","0","0","0","0.1026",{"$nulls":20},"3.207317","0.77","3.395","1","-2.71","1.0","0.007","0.904",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","162,0","0","162","0/1","78,11","0.1236","89",null,"chr1:3781561:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1228"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRRC70","chr5:62580813","LRRC70(P459S)",{"$nulls":6},255,"PASS","Missense","rs750179831",0.0004757,null,"FUNCTION: Renders cells highly sensitive to the activation by cytokines and lipopolysaccharide (LPS). {ECO:0000269|PubMed:12767927}.; ",{"$nulls":4},"p.Pro459Ser","c.1375C>T","MODERATE","459/622",2,{"$nulls":5},"5","406","324","308","243","342","275","0","0","0","0.16",{"$nulls":20},"0.098301","0.9",null,"1","0.55",null,"0.866","0.028",{"$nulls":3},"ExAC_AFR_AF",0.0004757,{"$nulls":7},"0/0","400,0","0","400","0/1","267,51","0.1604","318",null,"chr5:62580813:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1728"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LRRC70","chr5:62580813","LRRC70(P459S)",{"$nulls":6},255,"PASS","Missense","rs750179831",0.0004757,null,"FUNCTION: Renders cells highly sensitive to the activation by cytokines and lipopolysaccharide (LPS). {ECO:0000269|PubMed:12767927}.; ",{"$nulls":4},"p.Pro459Ser","c.1375C>T","MODERATE","459/622",2,{"$nulls":5},"4","406","428","308","325","341","371","0","0","0","0.0593",{"$nulls":20},"0.098301","0.9",null,"1","0.55",null,"0.866","0.028",{"$nulls":3},"ExAC_AFR_AF",0.0004757,{"$nulls":7},"0/0","390,0","0","390","0/1","387,26","0.063","413",null,"chr5:62580813:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0615"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRRIQ3","chr1:74109528","LRRIQ3(K244fs)",null,null,"domain (IQ ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Loss Of Function","rs764646737",-1,{"$nulls":6},"p.Lys244fs","c.732delA","HIGH","244/624",5,{"$nulls":5},"1",{"$nulls":15},"(LRRIQ3|ENSG00000162620|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","155,3","0.019","195","0/1","194,50","0.2049","288",null,"chr1:74109528:GT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LRRK2","chr12:40235682","LRRK2(G135A)",null,null,"region of interest (Required for RAB29-mediated activation )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Parkinson disease 8 (PARK8) [MIM:607060]: A slowly progressive neurodegenerative disorder characterized by bradykinesia, rigidity, resting tremor, postural instability, neuronal loss in the substantia nigra, and the presence of neurofibrillary MAPT (tau)-positive and Lewy bodies in some patients. {ECO:0000269|PubMed:15541308, ECO:0000269|PubMed:15541309, ECO:0000269|PubMed:15680455, ECO:0000269|PubMed:15680456, ECO:0000269|PubMed:15680457, ECO:0000269|PubMed:15726496, ECO:0000269|PubMed:15732108, ECO:0000269|PubMed:15811454, ECO:0000269|PubMed:15852371, ECO:0000269|PubMed:15880653, ECO:0000269|PubMed:15925109, ECO:0000269|PubMed:15929036, ECO:0000269|PubMed:16102999, ECO:0000269|PubMed:16157901, ECO:0000269|PubMed:16157908, ECO:0000269|PubMed:16157909, ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:16240353, ECO:0000269|PubMed:16247070, ECO:0000269|PubMed:16250030, ECO:0000269|PubMed:16251215, ECO:0000269|PubMed:16269541, ECO:0000269|PubMed:16272164, ECO:0000269|PubMed:16272257, ECO:0000269|PubMed:16298482, ECO:0000269|PubMed:16321986, ECO:0000269|PubMed:16333314, ECO:0000269|PubMed:16533964, ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18213618, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22956510, ECO:0000269|PubMed:23395371}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Positively regulates autophagy through a calcium- dependent activation of the CaMKK/AMPK signaling pathway. The process involves activation of nicotinic acid adenine dinucleotide phosphate (NAADP) receptors, increase in lysosomal pH, and calcium release from lysosomes. Together with RAB29, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner. Regulates neuronal process morphology in the intact central nervous system (CNS). Plays a role in synaptic vesicle trafficking. Phosphorylates PRDX3. Has GTPase activity. May play a role in the phosphorylation of proteins central to Parkinson disease. {ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18230735, ECO:0000269|PubMed:20949042, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22012985, ECO:0000269|PubMed:23395371, ECO:0000269|PubMed:24687852}.; ",{"$nulls":4},"p.Gly135Ala","c.404G>C","MODERATE","135/2527",4,{"$nulls":5},"5","660","484","433","324","574","400","0","0","0","0.1",{"$nulls":20},"2.7598570000000002","1.49",".;.;1.83","0.999103","-1.31;-1.83;-1.31",".;.;0.906","0.637;0.419;0.494",".;0.596;0.61",{"$nulls":3},"Unknown",-1,"AD","Parkinson disease 8; Dementia, Lewy body","Neurologic",{"$nulls":3},"C1846862","0/0","621,0","0","621","0/1","413,44","0.0963","457",null,"chr12:40235682:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0864"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LRRK2","chr12:40235682","LRRK2(G135A)",null,null,"region of interest (Required for RAB29-mediated activation )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Parkinson disease 8 (PARK8) [MIM:607060]: A slowly progressive neurodegenerative disorder characterized by bradykinesia, rigidity, resting tremor, postural instability, neuronal loss in the substantia nigra, and the presence of neurofibrillary MAPT (tau)-positive and Lewy bodies in some patients. {ECO:0000269|PubMed:15541308, ECO:0000269|PubMed:15541309, ECO:0000269|PubMed:15680455, ECO:0000269|PubMed:15680456, ECO:0000269|PubMed:15680457, ECO:0000269|PubMed:15726496, ECO:0000269|PubMed:15732108, ECO:0000269|PubMed:15811454, ECO:0000269|PubMed:15852371, ECO:0000269|PubMed:15880653, ECO:0000269|PubMed:15925109, ECO:0000269|PubMed:15929036, ECO:0000269|PubMed:16102999, ECO:0000269|PubMed:16157901, ECO:0000269|PubMed:16157908, ECO:0000269|PubMed:16157909, ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:16240353, ECO:0000269|PubMed:16247070, ECO:0000269|PubMed:16250030, ECO:0000269|PubMed:16251215, ECO:0000269|PubMed:16269541, ECO:0000269|PubMed:16272164, ECO:0000269|PubMed:16272257, ECO:0000269|PubMed:16298482, ECO:0000269|PubMed:16321986, ECO:0000269|PubMed:16333314, ECO:0000269|PubMed:16533964, ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18213618, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22956510, ECO:0000269|PubMed:23395371}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Positively regulates autophagy through a calcium- dependent activation of the CaMKK/AMPK signaling pathway. The process involves activation of nicotinic acid adenine dinucleotide phosphate (NAADP) receptors, increase in lysosomal pH, and calcium release from lysosomes. Together with RAB29, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner. Regulates neuronal process morphology in the intact central nervous system (CNS). Plays a role in synaptic vesicle trafficking. Phosphorylates PRDX3. Has GTPase activity. May play a role in the phosphorylation of proteins central to Parkinson disease. {ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18230735, ECO:0000269|PubMed:20949042, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22012985, ECO:0000269|PubMed:23395371, ECO:0000269|PubMed:24687852}.; ",{"$nulls":4},"p.Gly135Ala","c.404G>C","MODERATE","135/2527",4,{"$nulls":5},"5","660","627","433","411","578","520","0","0","0","0.0538",{"$nulls":20},"2.7598570000000002","1.49",".;.;1.83","0.999103","-1.31;-1.83;-1.31",".;.;0.906","0.637;0.419;0.494",".;0.596;0.61",{"$nulls":3},"Unknown",-1,"AD","Parkinson disease 8; Dementia, Lewy body","Neurologic",{"$nulls":3},"C1846862","0/0","627,0","0","627","0/1","568,37","0.0612","605",null,"chr12:40235682:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0584"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","LYRM5","chr12:25204100","LYRM5(L21V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Leu21Val","c.61C>G","MODERATE","21/90",3,{"$nulls":5},"5","169","187","132","145","125","135","0","0","0","0.1481",{"$nulls":20},"2.810307","-0.38;-0.38;-0.38;-0.38;-0.38;.",null,"1;1;1;1;1;1;1;1;0.963081","-2.25;-2.25;-2.25;-2.25;-2.25;-2.5",".;.;.;.;.;0.054","0.013;0.013;0.013;0.013;0.013;0.05","0.259;0.256;0.265;0.321;0.32;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","166,0","0","166","0/1","157,26","0.1421","183",null,"chr12:25204100:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1448"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","LYRM5","chr12:25204100","LYRM5(L21V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Leu21Val","c.61C>G","MODERATE","21/90",3,{"$nulls":5},"5","169","184","132","140","125","132","0","0","0","0.0606",{"$nulls":20},"2.810307","-0.38;-0.38;-0.38;-0.38;-0.38;.",null,"1;1;1;1;1;1;1;1;0.963081","-2.25;-2.25;-2.25;-2.25;-2.25;-2.5",".;.;.;.;.;0.054","0.013;0.013;0.013;0.013;0.013;0.05","0.259;0.256;0.265;0.321;0.32;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","166,0","0","166","0/1","167,12","0.067","179",null,"chr12:25204100:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0643"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MACF1","chr1:39447682","MACF1(Splicing Acceptor/Donor Loss)",null,null,"repeat (Spectrin 15 )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Isoform 2: F-actin-binding protein which plays a role in cross-linking actin to other cytoskeletal proteins and also binds to microtubules (PubMed:15265687, PubMed:20937854). Plays an important role in ERBB2-dependent stabilization of microtubules at the cell cortex (PubMed:20937854). Acts as a positive regulator of Wnt receptor signaling pathway and is involved in the translocation of AXIN1 and its associated complex (composed of APC, CTNNB1 and GSK3B) from the cytoplasm to the cell membrane (By similarity). Has actin-regulated ATPase activity and is essential for controlling focal adhesions (FAs) assembly and dynamics (By similarity). Interaction with CAMSAP3 at the minus ends of non- centrosomal microtubules tethers microtubules minus-ends to actin filaments, regulating focal adhesion size and cell migration (PubMed:27693509). May play role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with GOLGA4 (PubMed:15265687). Plays a key role in wound healing and epidermal cell migration (By similarity). Required for efficient upward migration of bulge cells in response to wounding and this function is primarily rooted in its ability to coordinate microtubule dynamics and polarize hair follicle stem cells (By similarity). {ECO:0000250|UniProtKB:Q9QXZ0, ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:20937854, ECO:0000269|PubMed:27693509}.; ",{"$nulls":4},"p.Val6625_Leu6650del","c.19873-9_19947delTTCCCTCAGGTTTTTGCTAATGAAGTAAATGCTCATCGAGACCAGATCATTGAGCTGGATCAAACTGGGAATCAATTAAAGTTC","HIGH","6625/7592",82,{"$nulls":20},"39447766",{"$nulls":26},"Unknown",-1,{"$nulls":6},"C5193029",{"$nulls":9},"chr1:39447682:GTTCCCTCAGGTTTTTGCTAATGAAGTAAATGCTCATCGAGACCAGATCATTGAGCTGGATCAAACTGGGAATCAATTAAAGTTC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf","structuralVariantFile","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MACF1","chr1:39447682","MACF1(Splicing Acceptor/Donor Loss)",null,null,"repeat (Spectrin 15 )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Isoform 2: F-actin-binding protein which plays a role in cross-linking actin to other cytoskeletal proteins and also binds to microtubules (PubMed:15265687, PubMed:20937854). Plays an important role in ERBB2-dependent stabilization of microtubules at the cell cortex (PubMed:20937854). Acts as a positive regulator of Wnt receptor signaling pathway and is involved in the translocation of AXIN1 and its associated complex (composed of APC, CTNNB1 and GSK3B) from the cytoplasm to the cell membrane (By similarity). Has actin-regulated ATPase activity and is essential for controlling focal adhesions (FAs) assembly and dynamics (By similarity). Interaction with CAMSAP3 at the minus ends of non- centrosomal microtubules tethers microtubules minus-ends to actin filaments, regulating focal adhesion size and cell migration (PubMed:27693509). May play role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with GOLGA4 (PubMed:15265687). Plays a key role in wound healing and epidermal cell migration (By similarity). Required for efficient upward migration of bulge cells in response to wounding and this function is primarily rooted in its ability to coordinate microtubule dynamics and polarize hair follicle stem cells (By similarity). {ECO:0000250|UniProtKB:Q9QXZ0, ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:20937854, ECO:0000269|PubMed:27693509}.; ",{"$nulls":4},"p.Val6625_Leu6650del","c.19873-9_19947delTTCCCTCAGGTTTTTGCTAATGAAGTAAATGCTCATCGAGACCAGATCATTGAGCTGGATCAAACTGGGAATCAATTAAAGTTC","HIGH","6625/7592",82,{"$nulls":20},"39447766",{"$nulls":26},"Unknown",-1,{"$nulls":6},"C5193029",{"$nulls":9},"chr1:39447682:GTTCCCTCAGGTTTTTGCTAATGAAGTAAATGCTCATCGAGACCAGATCATTGAGCTGGATCAAACTGGGAATCAATTAAAGTTC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf","structuralVariantFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MACF1","chr1:39447682","MACF1(Splicing Acceptor/Donor Loss)",null,null,"repeat (Spectrin 15 )",{"$nulls":3},838.362,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Isoform 2: F-actin-binding protein which plays a role in cross-linking actin to other cytoskeletal proteins and also binds to microtubules (PubMed:15265687, PubMed:20937854). Plays an important role in ERBB2-dependent stabilization of microtubules at the cell cortex (PubMed:20937854). Acts as a positive regulator of Wnt receptor signaling pathway and is involved in the translocation of AXIN1 and its associated complex (composed of APC, CTNNB1 and GSK3B) from the cytoplasm to the cell membrane (By similarity). Has actin-regulated ATPase activity and is essential for controlling focal adhesions (FAs) assembly and dynamics (By similarity). Interaction with CAMSAP3 at the minus ends of non- centrosomal microtubules tethers microtubules minus-ends to actin filaments, regulating focal adhesion size and cell migration (PubMed:27693509). May play role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with GOLGA4 (PubMed:15265687). Plays a key role in wound healing and epidermal cell migration (By similarity). Required for efficient upward migration of bulge cells in response to wounding and this function is primarily rooted in its ability to coordinate microtubule dynamics and polarize hair follicle stem cells (By similarity). {ECO:0000250|UniProtKB:Q9QXZ0, ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:20937854, ECO:0000269|PubMed:27693509}.; ",{"$nulls":4},"p.Val6625_Leu6650del","c.19873-9_19947delTTCCCTCAGGTTTTTGCTAATGAAGTAAATGCTCATCGAGACCAGATCATTGAGCTGGATCAAACTGGGAATCAATTAAAGTTC","HIGH","6625/7592",82,{"$nulls":5},"2",null,null,"401","259",{"$nulls":37},"Unknown",-1,{"$nulls":6},"C5193029","0/0","445,0","0","445","0/1","317,279","0.4681","596",null,"chr1:39447682:GTTCCCTCAGGTTTTTGCTAATGAAGTAAATGCTCATCGAGACCAGATCATTGAGCTGGATCAAACTGGGAATCAATTAAAGTTC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.7722"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MAMDC2","chr9:70143575","MAMDC2(T387R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr387Arg","c.1160C>G","MODERATE","387/686",9,{"$nulls":5},"4","346","377","262","300","265","294","0","0","0","0.3061",{"$nulls":20},"3.653228","4.26","2.64","0.999995","-3.3","0.997","0.032","0.825",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","323,0","0","323","0/1","247,113","0.3139","360",null,"chr9:70143575:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MAMDC2","chr9:70143575","MAMDC2(T387R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr387Arg","c.1160C>G","MODERATE","387/686",9,{"$nulls":5},"4","346","402","262","312","267","336","0","0","0","0.122",{"$nulls":20},"3.653228","4.26","2.64","0.999995","-3.3","0.997","0.032","0.825",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","323,0","0","323","0/1","337,48","0.1247","385",null,"chr9:70143575:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1378"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MAP3K7","chr6:90518472","MAP3K7(E539Q)",null,null,"splice variant (In isoform 1C and isoform 1D. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Frontometaphyseal dysplasia 2 (FMD2) [MIM:617137]: A form of frontometaphyseal dysplasia, a progressive sclerosing skeletal dysplasia affecting the long bones and skull. Characteristic features include supraorbital hyperostosis, cranial hyperostosis, undermodeling of the small bones, flared metaphyses, and digital anomalies. Extra-skeletal manifestations include hearing loss, cardiac malformations, and stenosis, particularly of the upper airway and urinary tract. FMD2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27426733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiospondylocarpofacial syndrome (CSCF) [MIM:157800]: A syndrome characterized by growth retardation, dysmorphic facial features, brachydactyly with carpal-tarsal fusion and extensive posterior cervical vertebral synostosis, cardiac septal defects with valve dysplasia, and deafness with inner ear malformations. CSCF transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27426734}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. Plays an important role in the cascades of cellular responses evoked by changes in the environment. Mediates signal transduction of TRAF6, various cytokines including interleukin-1 (IL-1), transforming growth factor-beta (TGFB), TGFB-related factors like BMP2 and BMP4, toll-like receptors (TLR), tumor necrosis factor receptor CD40 and B-cell receptor (BCR). Ceramides are also able to activate MAP3K7/TAK1. Once activated, acts as an upstream activator of the MKK/JNK signal transduction cascade and the p38 MAPK signal transduction cascade through the phosphorylation and activation of several MAP kinase kinases like MAP2K1/MEK1, MAP2K3/MKK3, MAP2K6/MKK6 and MAP2K7/MKK7. These MAP2Ks in turn activate p38 MAPKs, c-jun N-terminal kinases (JNKs) and I-kappa-B kinase complex (IKK). Both p38 MAPK and JNK pathways control the transcription factors activator protein-1 (AP-1), while nuclear factor-kappa B is activated by IKK. MAP3K7 activates also IKBKB and MAPK8/JNK1 in response to TRAF6 signaling and mediates BMP2- induced apoptosis. In osmotic stress signaling, plays a major role in the activation of MAPK8/JNK1, but not that of NF-kappa-B. Promotes TRIM5 capsid-specific restriction activity. {ECO:0000269|PubMed:10094049, ECO:0000269|PubMed:11460167, ECO:0000269|PubMed:12589052, ECO:0000269|PubMed:16845370, ECO:0000269|PubMed:16893890, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:8663074, ECO:0000269|PubMed:9079627}.; ","level2",{"$nulls":3},"p.Glu539Gln","c.1615G>C","MODERATE","539/606",16,{"$nulls":5},"5","107","131","85","112","62","94","0","0","0","0.0957",{"$nulls":20},"3.7120480000000002","-1.68;-1.44;.",".;2.25;.","1","-1.04;-1.11;-2.69","0.035;0.993;.","0.228;0.131;0.002","0.773;0.657;0.836",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK,kWNT",null,null,"C2931461| C4310697","0/0","103,0","0","103","0/1","119,11","0.0846","130",null,"chr6:90518472:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0982"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MAP3K7","chr6:90518472","MAP3K7(E539Q)",null,null,"splice variant (In isoform 1C and isoform 1D. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Frontometaphyseal dysplasia 2 (FMD2) [MIM:617137]: A form of frontometaphyseal dysplasia, a progressive sclerosing skeletal dysplasia affecting the long bones and skull. Characteristic features include supraorbital hyperostosis, cranial hyperostosis, undermodeling of the small bones, flared metaphyses, and digital anomalies. Extra-skeletal manifestations include hearing loss, cardiac malformations, and stenosis, particularly of the upper airway and urinary tract. FMD2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27426733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiospondylocarpofacial syndrome (CSCF) [MIM:157800]: A syndrome characterized by growth retardation, dysmorphic facial features, brachydactyly with carpal-tarsal fusion and extensive posterior cervical vertebral synostosis, cardiac septal defects with valve dysplasia, and deafness with inner ear malformations. CSCF transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27426734}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. Plays an important role in the cascades of cellular responses evoked by changes in the environment. Mediates signal transduction of TRAF6, various cytokines including interleukin-1 (IL-1), transforming growth factor-beta (TGFB), TGFB-related factors like BMP2 and BMP4, toll-like receptors (TLR), tumor necrosis factor receptor CD40 and B-cell receptor (BCR). Ceramides are also able to activate MAP3K7/TAK1. Once activated, acts as an upstream activator of the MKK/JNK signal transduction cascade and the p38 MAPK signal transduction cascade through the phosphorylation and activation of several MAP kinase kinases like MAP2K1/MEK1, MAP2K3/MKK3, MAP2K6/MKK6 and MAP2K7/MKK7. These MAP2Ks in turn activate p38 MAPKs, c-jun N-terminal kinases (JNKs) and I-kappa-B kinase complex (IKK). Both p38 MAPK and JNK pathways control the transcription factors activator protein-1 (AP-1), while nuclear factor-kappa B is activated by IKK. MAP3K7 activates also IKBKB and MAPK8/JNK1 in response to TRAF6 signaling and mediates BMP2- induced apoptosis. In osmotic stress signaling, plays a major role in the activation of MAPK8/JNK1, but not that of NF-kappa-B. Promotes TRIM5 capsid-specific restriction activity. {ECO:0000269|PubMed:10094049, ECO:0000269|PubMed:11460167, ECO:0000269|PubMed:12589052, ECO:0000269|PubMed:16845370, ECO:0000269|PubMed:16893890, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:8663074, ECO:0000269|PubMed:9079627}.; ","level2",{"$nulls":3},"p.Glu539Gln","c.1615G>C","MODERATE","539/606",16,{"$nulls":5},"4","107","138","85","115",null,null,"0","0",{"$nulls":22},"3.7120480000000002","-1.68;-1.44;.",".;2.25;.","1","-1.04;-1.11;-2.69","0.035;0.993;.","0.228;0.131;0.002","0.773;0.657;0.836",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK,kWNT",null,null,"C2931461| C4310697","0/0","103,0","0","103","0/1","128,8","0.0588","136",null,"chr6:90518472:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0609"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MB21D2","chr3:192798808","MB21D2(D352H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp352His","c.1054G>C","MODERATE","352/491",2,{"$nulls":5},"4","600","765","484","611","536","693","0","0","0","0.1299",{"$nulls":20},"3.75963","3.1","1.78","1","-2.94","1.0","0.005","0.706",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","599,0","0","599","0/1","660,94","0.1247","754",null,"chr3:192798808:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1244"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MB21D2","chr3:192798808","MB21D2(D352H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp352His","c.1054G>C","MODERATE","352/491",2,{"$nulls":5},"4","600","856","484","665","536","748","0","0","0","0.0575",{"$nulls":20},"3.75963","3.1","1.78","1","-2.94","1.0","0.005","0.706",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","603,0","0","603","0/1","797,46","0.0546","843",null,"chr3:192798808:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0511"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MDN1","chr6:89692757","MDN1(S3425C)",null,null,"region of interest (Linker )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits (PubMed:27814492). Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre- 60S particles from the nucleolus and then driving late pre-60S particles from the nucleus (By similarity). At an early stage in 60S maturation, mediates the dissociation of the PeBoW complex (PES1-BOP1-WDR12) from early pre-60S particles, rendering them competent for export from the nucleolus to the nucleoplasm (By similarity). Subsequently recruited to the nucleoplasmic particles through interaction with SUMO-conjugated PELP1 complex (PubMed:27814492). This binding is only possible if the 5S RNP at the central protuberance has undergone the rotation to complete its maturation (By similarity). {ECO:0000250|UniProtKB:Q12019, ECO:0000269|PubMed:27814492}.; ",{"$nulls":4},"p.Ser3425Cys","c.10273A>T","MODERATE","3425/5596",63,{"$nulls":5},"5","704","752","539","568","632","658","0","0","0","0.1429",{"$nulls":20},"0.819441","3.91;.","2.14","1","-2.48;.","0.953","0.039;.","0.17;0.213",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","680,0","0","680","0/1","630,109","0.1475","739",null,"chr6:89692757:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1479"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MDN1","chr6:89692757","MDN1(S3425C)",null,null,"region of interest (Linker )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits (PubMed:27814492). Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre- 60S particles from the nucleolus and then driving late pre-60S particles from the nucleus (By similarity). At an early stage in 60S maturation, mediates the dissociation of the PeBoW complex (PES1-BOP1-WDR12) from early pre-60S particles, rendering them competent for export from the nucleolus to the nucleoplasm (By similarity). Subsequently recruited to the nucleoplasmic particles through interaction with SUMO-conjugated PELP1 complex (PubMed:27814492). This binding is only possible if the 5S RNP at the central protuberance has undergone the rotation to complete its maturation (By similarity). {ECO:0000250|UniProtKB:Q12019, ECO:0000269|PubMed:27814492}.; ",{"$nulls":4},"p.Ser3425Cys","c.10273A>T","MODERATE","3425/5596",63,{"$nulls":5},"5","704","785","539","596","632","696","0","0","0","0.0575",{"$nulls":20},"0.819441","3.91;.","2.14","1","-2.48;.","0.953","0.039;.","0.17;0.213",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","675,0","0","675","0/1","732,46","0.0591","778",null,"chr6:89692757:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0554"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MED26","chr19:16577229","MED26(H201N)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional pre-initiation complex with RNA polymerase II and the general transcription factors.; ",{"$nulls":4},"p.His201Asn","c.601C>A","MODERATE","201/600",3,{"$nulls":5},"5","462","375","318","274","414","328","0","0","0","0.3232",{"$nulls":20},"1.856439",null,null,"1;0.997771",{"$nulls":3},"0.38",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","447,0","0","447","0/1","244,121","0.3315","365",null,"chr19:16577229:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3394"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MED26","chr19:16577229","MED26(H201N)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional pre-initiation complex with RNA polymerase II and the general transcription factors.; ",{"$nulls":4},"p.His201Asn","c.601C>A","MODERATE","201/600",3,{"$nulls":5},"5","462","489","318","342","417","433","0","0","0","0.1547",{"$nulls":20},"1.856439",null,null,"1;0.997771",{"$nulls":3},"0.38",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","447,0","0","447","0/1","399,77","0.1618","476",null,"chr19:16577229:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MEGF8","chr19:42360784","MEGF8(S1833F)",null,null,"topological domain (Extracellular ), repeat (Kelch 11 )",{"$nulls":3},255,"PASS","Missense","rs759962028",0.002683,"DISEASE: Carpenter syndrome 2 (CRPT2) [MIM:614976]: An autosomal recessive multiple congenital malformation disorder characterized by multisuture craniosynostosis and polysyndactyly of the hands and feet, in association with abnormal left-right patterning and other features, most commonly obesity, umbilical hernia, cryptorchidism, and congenital heart disease. {ECO:0000269|PubMed:23063620}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a negative regulator of hedgehog signaling. {ECO:0000250|UniProtKB:P60882}.; ",{"$nulls":4},"p.Ser1833Phe","c.5498C>T","MODERATE","1833/2845",32,{"$nulls":5},"5","111","126","92","99","88","106","0","0","0","0.1509",{"$nulls":20},"2.370195","-0.36",".;0.97","0.97484;0.966313","-2.2","0.0;0.979","0.224;0.732","0.293;0.246",{"$nulls":3},"ExAC_AMR_AF",0.002683,"AR","Carpenter syndrome 2","Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal ",{"$nulls":3},"C3554247","0/0","113,0","0","113","0/1","107,18","0.144","125",null,"chr19:42360784:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1515"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MESDC2","chr15:80989677","MESDC2(G39R)",{"$nulls":6},255,"PASS","Missense","rs1428605286",-1,{"$nulls":6},"p.Gly39Arg","c.115G>C","MODERATE","39/234",1,{"$nulls":5},"5","399","362","285","261","324","286","0","0","0","0.1643",{"$nulls":20},"0.864759",null,"0.805","0.983238","-1.0","0.009","0.401","0.221;0.202",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","378,0","0","378","0/1","280,52","0.1566","332",null,"chr15:80989677:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1609"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MESDC2","chr15:80989677","MESDC2(G39R)",{"$nulls":6},255,"PASS","Missense","rs1428605286",-1,{"$nulls":6},"p.Gly39Arg","c.115G>C","MODERATE","39/234",1,{"$nulls":5},"5","399","478","285","355","325","385","0","0","0","0.0571",{"$nulls":20},"0.864759",null,"0.805","0.983238","-1.0","0.009","0.401","0.221;0.202",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","377,0","0","377","0/1","435,28","0.0605","463",null,"chr15:80989677:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0592"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MSH4","chr1:75883710","MSH4(N666H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in meiotic recombination. Required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis.; ",{"$nulls":4},"p.Asn666His","c.1996A>C","MODERATE","666/936",15,{"$nulls":5},"5","223","242","156","172","187","208","0","0","0","0.1635",{"$nulls":20},"2.607133","-2.12","1.97","0.99736","-3.17","0.304","0.006","0.825",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","215,0","0","215","0/1","201,38","0.159","239",null,"chr1:75883710:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1628"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MSH4","chr1:75883710","MSH4(N666H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in meiotic recombination. Required for reciprocal recombination and proper segregation of homologous chromosomes at meiosis.; ",{"$nulls":4},"p.Asn666His","c.1996A>C","MODERATE","666/936",15,{"$nulls":5},"5","223","272","156","197","190","225","0","0","0","0.0578",{"$nulls":20},"2.607133","-2.12","1.97","0.99736","-3.17","0.304","0.006","0.825",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","215,0","0","215","0/1","251,17","0.0634","268",null,"chr1:75883710:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0711"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC1","chr1:155189697","MUC1(P653A)",null,null,"topological domain (Extracellular ), repeat (30 ), region of interest (42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R ), splice variant (In isoform E2. ), splice variant (In isoform T10. ), splice variant (In isoform J13, isoform Y, isoform Y-LSP and isoform S2. ), splice variant (In isoform 8, isoform 9 and isoform M6. ), splice variant (In isoform 6. ), splice variant (In isoform F. ), splice variant (In isoform ZD. )",{"$nulls":3},44,"PASS","Missense",null,-1,"DISEASE: Note=MUC1/CA 15-3 is used as a serological clinical marker of breast cancer to monitor response to breast cancer treatment and disease recurrence (PubMed:20816948). Decreased levels over time may be indicative of a positive response to treatment. Conversely, increased levels may indicate disease progression. At an early stage disease, only 21% of patients exhibit high MUC1/CA 15-3 levels, that is why CA 15-3 is not a useful screening test. Most antibodies target the highly immunodominant core peptide domain of 20 amino acid (APDTRPAPGSTAPPAHGVTS) tandem repeats. Some antibodies recognize glycosylated epitopes. {ECO:0000269|PubMed:20816948}.; DISEASE: Medullary cystic kidney disease 1 (MCKD1) [MIM:174000]: A form of tubulointerstitial nephropathy characterized by formation of renal cysts at the corticomedullary junction. It is characterized by adult onset of impaired renal function and salt wasting resulting in end-stage renal failure by the sixth decade. {ECO:0000269|PubMed:23396133}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The alpha subunit has cell adhesive properties. Can act both as an adhesion and an anti-adhesion protein. May provide a protective layer on epithelial cells against bacterial and enzyme attack.; ","level2",{"$nulls":3},"p.Pro653Ala","c.1957C>G","MODERATE","653/1262",5,{"$nulls":5},"1",{"$nulls":30},"-0.424685",null,null,"0.999995",{"$nulls":3},"0.095",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1868139","0/0","22,0","0","22","0/1","19,3","0.1364","22",null,"chr1:155189697:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1364"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC16","chr19:8910431","MUC16(G12406R)",null,null,"topological domain (Extracellular ), repeat (3 ), domain (SEA 3 ), region of interest (12 X approximate tandem repeats )",{"$nulls":3},177,"PASS","Missense","rs75219945",0.0081799591002045,null,"FUNCTION: Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. {ECO:0000250}.; ",{"$nulls":4},"p.Gly12406Arg","c.37216G>C","MODERATE","12406/14507",19,22,{"$nulls":4},"1",{"$nulls":30},"-1.09889","1.56",null,"1","-2.49",null,"0.126","0.112",{"$nulls":3},"1000Gp3_SAS_AF",0.0081799591002045,{"$nulls":7},"0/0","377,0","0","419","0/1","372,28","0.0675","415",null,"chr19:8910431:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0675"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC16","chr19:8896017","MUC16(T13161_G13185delinsSLALSTerYHSLSTLPSPTCIMKKTC???)",null,null,"topological domain (Extracellular ), repeat (8 ), region of interest (12 X approximate tandem repeats )","glycosylation-site:N-linked_(GlcNAc...), domain:SEA_8, repeat:8","MODERATE, LOW, LOW",null,160,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. {ECO:0000250}.; ",{"$nulls":4},"p.Thr13161_Gly13185delinsSerLeuAlaLeuSerTerTyrHisSerLeuSerThrLeuProSerProThrCysIleMetLysLysThrCys???","c.39482-14_39555delCACCTTCACTATAGCCACCGGCCCTCTCCTGGTGCCATTCACACTCAACTTCACCATCACTAACCTACAGTATGAGGAGAACATGGGTinsAACCGCTTTACAGAGCCTGGCCCTCTCCTGATACCATTCACTTTCAACTTTACCATCACCAACCTGCATTATGAAGAAAACATGCAA","HIGH","13161/14507",44,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","395,0","0","395","0/1","330,21","0.0597","352",null,"chr19:8896017:ACCCATGTTCTCCTCATACTGTAGGTTAGTGATGGTGAAGTTGAGTGTGAATGGCACCAGGAGAGGGCCGGTGGCTATAGTGAAGGTG:TTGCATGTTTTCTTCATAATGCAGGTTGGTGATGGTAAAGTTGAAAGTGAATGGTATCAGGAGAGGGCCAGGCTCTGTAAAGCGGTT",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0597"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC20","chr3:195725626","MUC20(S342fs)",null,null,"repeat (9 ), region of interest (12 X 20 AA approximate tandem repeats of S-S-E-S-S-A-S-S-D-S-P-H-P-V-I-T-P-S-R-A ), compositionally biased region (Ser-rich ), sequence variant , sequence variant , sequence variant , sequence variant ",{"$nulls":3},103,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May regulate MET signaling cascade. Seems to decrease hepatocyte growth factor (HGF)-induced transient MAPK activation. Blocks GRB2 recruitment to MET thus suppressing the GRB2-RAS pathway. Inhibits HGF-induced proliferation of MMP1 and MMP9 expression. {ECO:0000269|PubMed:15314156}.; ",{"$nulls":4},"p.Ser342fs","c.1023_1034del<DELETE_NUC>insG","HIGH","342/723",2,{"$nulls":5},"1",{"$nulls":14},"195725798",{"$nulls":26},"Unknown",-1,{"$nulls":7},"0/0","11,0","0","11","0/1","16,7","0.3684","19",null,"chr3:195725626:<DELETE_NUC>:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3684"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC3A","chr7:100953321","MUC3A(V515_M539delinsTSTENTPTWSLLTSFPMTHSFSSI)",null,null,"compositionally biased region (Thr-rich ), compositionally biased region (Ser-rich )",{"$nulls":3},208,"PASS","Missense",null,-1,null,"FUNCTION: Major glycoprotein component of a variety of mucus gels. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. May be involved in ligand binding and intracellular signaling. {ECO:0000269|PubMed:10405327}.; ",{"$nulls":4},"p.Val515_Met539delinsThrSerThrGluAsnThrProThrTrpSerLeuLeuThrSerPheProMetThrHisSerPheSerSerIle","c.1542_1617delTGTAAGTACACTCAGCACTCCTACAAGTTCCCTCCTGACGACCTTCCCAGCAACATATTCATTTTCATCTTCCATGinsCACAAGTACTGAGAACACTCCAACATGGTCCCTCCTGACAAGCTTTCCAATGACACATTCGTTCTCTTCTATT","MODERATE","514/3323",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","767,0","0","827","0/1","621,52","0.0773","673",null,"chr7:100953321:TGTAAGTACACTCAGCACTCCTACAAGTTCCCTCCTGACGACCTTCCCAGCAACATATTCATTTTCATCTTCCATG:CACAAGTACTGAGAACACTCCAACATGGTCCCTCCTGACAAGCTTTCCAATGACACATTCGTTCTCTTCTATT",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0773"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC3A","chr7:100957964","MUC3A(Insert)",{"$nulls":6},240,"PASS","Large Insertion",{"$nulls":3},"FUNCTION: Major glycoprotein component of a variety of mucus gels. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. May be involved in ligand binding and intracellular signaling. {ECO:0000269|PubMed:10405327}.; ",{"$nulls":14},"1",{"$nulls":14},"1.00958067E8",{"$nulls":35},"0/0","1879,0","0","2349","0/1","886,261","0.1261","2070",null,"MUC3A_gain",0,0,"LargeInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor",null,"0.1261"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195779303","MUC4(H4093D)",{"$nulls":6},255,"PASS","Missense","rs1382861183",-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.His4093Asp","c.12277C>G","MODERATE","4093/5412",2,{"$nulls":5},"1",{"$nulls":30},"0.068481","1.55",null,"1","-0.47;-0.63",null,"1.0","0.173;0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","28,0","0","30","0/1","17,5","0.2273","29",null,"chr3:195779303:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195779611","MUC4(DT3989SL)",{"$nulls":6},150,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.AspThr3989SerLeu","c.11965_11969delGACACinsAGCCT","MODERATE","3989/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","73,0","0","86","0/1","91,18","0.1525","118",null,"chr3:195779611:GTGTC:AGGCT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1525"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195780044","MUC4(IP3845DA)",{"$nulls":6},99,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.IlePro3845AspAla","c.11533_11536delATCCinsGACG","MODERATE","3845/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","21,0","0","38","0/1","28,8","0.16","50",null,"chr3:195780044:GGAT:CGTC",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.16"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195781244","MUC4(ST3445DA)",{"$nulls":6},174,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.SerThr3445AspAla","c.10333_10336delAGCAinsGACG","MODERATE","3445/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","166,0","0","195","0/1","192,31","0.1211","256",null,"chr3:195781244:TGCT:CGTC",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1211"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195782146","MUC4(P3122_A3145delinsLVTDASSL)",{"$nulls":6},239,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.Pro3122_Ala3145delinsLeuValThrAspAlaSerSerLeu","c.9365_9434delCTGTCACCGACACTTCCTCAGCATCCACAGGTCAGGCCACCGCTCTTCCTGTCACCAGCACTTCCTCAGCinsTTGTCACCGATGCTTCCTCATT","MODERATE","3122/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","1531,0","0","1585","0/1","1792,108","0.0535","2019",null,"chr3:195782146:GCTGAGGAAGTGCTGGTGACAGGAAGAGCGGTGGCCTGACCTGTGGATGCTGAGGAAGTGTCGGTGACAG:AATGAGGAAGCATCGGTGACAA",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0535"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195785371","MUC4(NP2069SL)",{"$nulls":6},129,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.AsnPro2069SerLeu","c.6204_6209delTAACCCinsCAGCCT","MODERATE","2068/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","17,0","0","19","0/1","18,17","0.4474","38",null,"chr3:195785371:GGGTTA:AGGCTG",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.4474"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195785771","MUC4(L1921_L1937delinsV)",{"$nulls":6},248,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.Leu1921_Leu1937delinsVal","c.5761_5809delCTTCCTGTCACCAGCCTTTCCTCAGCATCCACAGGTGACACCACGCCTCinsG","MODERATE","1921/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","1292,0","0","1414","0/1","1444,123","0.0783","1571",null,"chr3:195785771:GAGGCGTGGTGTCACCTGTGGATGCTGAGGAAAGGCTGGTGACAGGAAG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0783"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC4","chr3:195787858","MUC4(V1225_A1240del)",{"$nulls":6},129,"PASS","Inframe Indel",null,-1,null,"FUNCTION: May play a role in tumor progression. Ability to promote tumor growth may be mainly due to repression of apoptosis as opposed to proliferation. Has anti-adhesive properties. Seems to alter cellular behavior through both anti-adhesive effects on cell-cell and cell-extracellular matrix interactions and in its ability to act as an intramembrane ligand for ERBB2. Plays an important role in cell proliferation and differentiation of epithelial cells by inducing specific phosphorylation of ERBB2. The MUC4-ERBB2 complex causes site-specific phosphorylation of the ERBB2 'Tyr-1248'. In polarized epithelial cells segregates ERBB2 and other ERBB receptors and prevents ERBB2 from acting as a coreceptor. The interaction with ERBB2 leads to enhanced expression of CDKN1B. The formation of a MUC4-ERBB2-ERBB3-NRG1 complex leads to down-regulation of CDKN1B, resulting in repression of apoptosis and stimulation of proliferation. {ECO:0000269|PubMed:12102554, ECO:0000269|PubMed:16049287, ECO:0000269|PubMed:16814944, ECO:0000269|PubMed:16914178}.; ",{"$nulls":4},"p.Val1225_Ala1240del","c.3674_3721delTGTCCACAGATCACGCCACCTCTCTTCCTGTAACCATCCCTTCCGCAG","MODERATE","1225/5412",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","10,0","0","10","0/1","12,12","0.5","24",null,"chr3:195787858:GCTGCGGAAGGGATGGTTACAGGAAGAGAGGTGGCGTGATCTGTGGACA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.5"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC5B","chr11:1243098","MUC5B(P2073L)",null,null,"region of interest (7 X Cys-rich subdomain repeats ), region of interest (11 X approximate tandem repeats, Ser/Thr-rich ), compositionally biased region (Thr-rich ), disulfide bond , sequence conflict (In Ref. 4; CAA96577. )",{"$nulls":3},73,"PASS","Missense","rs199699804",0.004449,"DISEASE: Pulmonary fibrosis, idiopathic (IPF) [MIM:178500]: A lung disease characterized by shortness of breath, radiographically evident diffuse pulmonary infiltrates, and varying degrees of inflammation and fibrosis on biopsy. In some cases, the disorder can be rapidly progressive and characterized by sequential acute lung injury with subsequent scarring and end-stage lung disease. {ECO:0000269|PubMed:21506741, ECO:0000269|PubMed:21506748}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. A common polymorphism in the promoter of MUC5B is associated with familial interstitial pneumonia and idiopathic pulmonary fibrosis, suggesting that dysregulated MUC5B expression in the lung may be involved in the pathogenesis of pulmonary fibrosis (PubMed:21506741). {ECO:0000269|PubMed:21506741}.; ","FUNCTION: Gel-forming mucin that is thought to contribute to the lubricating and viscoelastic properties of whole saliva and cervical mucus.; ",{"$nulls":4},"p.Pro2073Leu","c.6218C>T","MODERATE","2073/5762",31,1,{"$nulls":4},"1",{"$nulls":30},"0.027456","2.26","-0.15","1","-0.3",null,"0.363","0.051",{"$nulls":3},"ExAC_FIN_AF",0.004449,{"$nulls":6},"C1800706","0/0","105,0","0","130","0/1","60,5","0.0714","70",null,"chr11:1243098:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0714"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC6","chr11:1017461","MUC6(G1777fs)",{"$nulls":6},265,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May provide a mechanism for modulation of the composition of the protective mucus layer related to acid secretion or the presence of bacteria and noxious agents in the lumen. Plays an important role in the cytoprotection of epithelial surfaces and are used as tumor markers in a variety of cancers. May play a role in epithelial organogenesis. {ECO:0000269|PubMed:10209489, ECO:0000269|PubMed:10330458, ECO:0000269|PubMed:11988092}.; ",{"$nulls":4},"p.Gly1777fs","c.5329_5340del>GAN_EAELED<insTGGGACA","HIGH","1777/2439",31,{"$nulls":5},"1",{"$nulls":14},"1017633",{"$nulls":26},"Unknown",-1,{"$nulls":7},"0/0","1212,0","0","1216","0/1","745,155","0.1788","867",null,"chr11:1017461:<DELETE_NUC>:TGTCCCA",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1788"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC6","chr11:1017032","MUC6(SPSSFSTAKTSTSLPYHT1905ALSSFSTAKTSTSLHSHA)",{"$nulls":6},206,"PASS","Missense",null,-1,null,"FUNCTION: May provide a mechanism for modulation of the composition of the protective mucus layer related to acid secretion or the presence of bacteria and noxious agents in the lumen. Plays an important role in the cytoprotection of epithelial surfaces and are used as tumor markers in a variety of cancers. May play a role in epithelial organogenesis. {ECO:0000269|PubMed:10209489, ECO:0000269|PubMed:10330458, ECO:0000269|PubMed:11988092}.; ",{"$nulls":4},"p.SerProSerSerPheSerThrAlaLysThrSerThrSerLeuProTyrHisThr1905AlaLeuSerSerPheSerThrAlaLysThrSerThrSerLeuHisSerHisAla","c.5713_5769delTCCCCAAGCTCATTTAGCACGGCCAAAACTTCTACATCCCTACCTTACCACACTTCCinsGCCCTGAGCTCTTTCAGCACAGCCAAAACCTCCACATCCCTACACTCACATGCTTCT","MODERATE","1905/2439",31,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","1643,0","0","1645","0/1","949,52","0.0519","1002",null,"chr11:1017032:GGAAGTGTGGTAAGGTAGGGATGTAGAAGTTTTGGCCGTGCTAAATGAGCTTGGGGA:AGAAGCATGTGAGTGTAGGGATGTGGAGGTTTTGGCTGTGCTGAAAGAGCTCAGGGC",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0519"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUC6","chr11:1017068","MUC6(PTTSGTSQSPSSFS1897ATTIQTSKAHNSFN)",{"$nulls":6},216,"PASS","Missense",null,-1,null,"FUNCTION: May provide a mechanism for modulation of the composition of the protective mucus layer related to acid secretion or the presence of bacteria and noxious agents in the lumen. Plays an important role in the cytoprotection of epithelial surfaces and are used as tumor markers in a variety of cancers. May play a role in epithelial organogenesis. {ECO:0000269|PubMed:10209489, ECO:0000269|PubMed:10330458, ECO:0000269|PubMed:11988092}.; ",{"$nulls":4},"p.ProThrThrSerGlyThrSerGlnSerProSerSerPheSer1897AlaThrThrIleGlnThrSerLysAlaHisAsnSerPheAsn","c.5688_5733delACCGACCACCAGTGGGACCAGCCAATCCCCAAGCTCATTTAGCACGinsGGCAACCACCATTCAGACAAGCAAAGCTCACAACTCATTCAACACA","MODERATE","1896/2439",31,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","1549,0","0","1677","0/1","971,63","0.0575","1096",null,"chr11:1017068:CGTGCTAAATGAGCTTGGGGATTGGCTGGTCCCACTGGTGGTCGGT:TGTGTTGAATGAGTTGTGAGCTTTGCTTGTCTGAATGGTGGTTGCC",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0575"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MUM1L1","chrX:106206132","MUM1L1(E234K)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu234Lys","c.700G>A","MODERATE","234/696",5,3,{"$nulls":4},"5","425","415","329","301","376","359","0","0","0","0.1086",{"$nulls":20},"2.60346","1.72",null,"1","-1.15",null,"0.04","0.282;0.28;0.283",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","427,0","0","427","0/1","360,49","0.1198","409",null,"chrX:106206132:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1063"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MYH10","chr17:8509841","MYH10(L1021F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Associated with severe intellectual disability, microcephaly, and feeding difficulties as well as cerebral atrophy. {ECO:0000269|PubMed:25003005, ECO:0000269|PubMed:25356899}.; ","FUNCTION: Cellular myosin that appears to play a role in cytokinesis, cell shape, and specialized functions such as secretion and capping. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. During cell spreading, plays an important role in cytoskeleton reorganization, focal contacts formation (in the central part but not the margins of spreading cells), and lamellipodial extension; this function is mechanically antagonized by MYH9. {ECO:0000269|PubMed:20052411, ECO:0000269|PubMed:20603131}.; ",{"$nulls":4},"p.Leu1021Phe","c.3061C>T","MODERATE","1021/2007",25,{"$nulls":5},"4","629","469","419","319","518","410","0","0","0","0.1707",{"$nulls":20},"3.527518","-2.48;.;-2.48",".;.;3.39","0.999815","-2.4;.;-2.4",".;.;0.715","0.017;.;0.041","0.513;0.546;0.556",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the myosin superfamily. The protein represents a conventional non-muscle myosin; it should not be confused with the unconventional myosin-10 (MYO10). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene have been associated with May-Hegglin anomaly and developmental defects in brain and heart. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011].",null,null,"0/0","603,0","0","603","0/1","378,77","0.1692","455",null,"chr17:8509841:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.163"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MYH15","chr3:108439895","MYH15(E993K)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs1262927327",-1,null,"FUNCTION: Muscle contraction. {ECO:0000250}.; ",{"$nulls":4},"p.Glu993Lys","c.2977G>A","MODERATE","993/1946",25,{"$nulls":5},"5","223","297","157","195","210","259","0","0","0","0.1467",{"$nulls":20},"3.755356","-2.93","2.885","0.999999","-3.48","1.0","0.001","0.684",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","222,0","0","222","0/1","237,53","0.1828","290",null,"chr3:108439895:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MYOF","chr10:93452075","MYOF(D71Y)",null,null,"topological domain (Cytoplasmic ), domain (C2 1 ), splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium/phospholipid-binding protein that plays a role in the plasmalemma repair mechanism of endothelial cells that permits rapid resealing of membranes disrupted by mechanical stress. Involved in endocytic recycling. Implicated in VEGF signal transduction by regulating the levels of the receptor KDR (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp71Tyr","c.211G>T","MODERATE","71/2061",3,{"$nulls":5},"5","185","121","134","85","155","93","0","0","0","0.1828",{"$nulls":20},"4.064264","0.22","4.37","0.999999;0.999999;0.999999;1;0.999999;0.999999","-6.26;-6.26;-7.11;-8.65","1.0;1.0;.;.","0.0","0.923;0.953;0.966;0.971",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Mutations in dysferlin, a protein associated with the plasma membrane, can cause muscle weakness that affects both proximal and distal muscles. The protein encoded by this gene is a type II membrane protein that is structurally similar to dysferlin. It is a member of the ferlin family and associates with both plasma and nuclear membranes. The protein contains C2 domains that play a role in calcium-mediated membrane fusion events, suggesting that it may be involved in membrane regeneration and repair. Two transcript variants encoding different isoforms have been found for this gene. Other possible variants have been detected, but their full-length nature has not been determined. [provided by RefSeq, Dec 2008].",null,null,"0/0","178,0","0","178","0/1","99,21","0.175","120",null,"chr10:93452075:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1412"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","MYOF","chr10:93452075","MYOF(D71Y)",null,null,"topological domain (Cytoplasmic ), domain (C2 1 ), splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium/phospholipid-binding protein that plays a role in the plasmalemma repair mechanism of endothelial cells that permits rapid resealing of membranes disrupted by mechanical stress. Involved in endocytic recycling. Implicated in VEGF signal transduction by regulating the levels of the receptor KDR (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp71Tyr","c.211G>T","MODERATE","71/2061",3,{"$nulls":5},"5","185","165","134","116","154","135","0","0","0","0.0815",{"$nulls":20},"4.064264","0.22","4.37","0.999999;0.999999;0.999999;1;0.999999;0.999999","-6.26;-6.26;-7.11;-8.65","1.0;1.0;.;.","0.0","0.923;0.953;0.966;0.971",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Mutations in dysferlin, a protein associated with the plasma membrane, can cause muscle weakness that affects both proximal and distal muscles. The protein encoded by this gene is a type II membrane protein that is structurally similar to dysferlin. It is a member of the ferlin family and associates with both plasma and nuclear membranes. The protein contains C2 domains that play a role in calcium-mediated membrane fusion events, suggesting that it may be involved in membrane regeneration and repair. Two transcript variants encoding different isoforms have been found for this gene. Other possible variants have been detected, but their full-length nature has not been determined. [provided by RefSeq, Dec 2008].",null,null,"0/0","178,0","0","178","0/1","145,13","0.0823","158",null,"chr10:93452075:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.069"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","MZF1","chr19:58563316","MZF1(D321Y)",null,null,"compositionally biased region (Asp/Glu-rich (acidic) ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1410305517",-1,null,"FUNCTION: Binds to target promoter DNA and functions as transcription regulator. Regulates transcription from the PADI1 and CDH2 promoter. May be one regulator of transcriptional events during hemopoietic development. {ECO:0000269|PubMed:15541732, ECO:0000269|PubMed:17851584}.; ",{"$nulls":4},"p.Asp321Tyr","c.961G>T","MODERATE","321/734",6,{"$nulls":5},"4","402","300","307","239","323","240","0.0025","0.0025","0","0.1125",{"$nulls":20},"2.401909","3.25","0.345","0.988689","-0.85;.","0.986","0.114;.","0.37;0.377",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","385,1","0.0026","386","0/1","252,38","0.131","290",null,"chr19:58563316:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1423"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NAGK","chr2:71075561","NAGK(D242Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Converts endogenous N-acetylglucosamine (GlcNAc), a major component of complex carbohydrates, from lysosomal degradation or nutritional sources into GlcNAc 6-phosphate. Involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway: although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded. Also has ManNAc kinase activity. {ECO:0000269|PubMed:22692205}.; ",{"$nulls":4},"p.Asp242Tyr","c.724G>T","MODERATE","242/390",7,{"$nulls":5},"5","385","601","285","430","327","497","0","0","0","0.1368",{"$nulls":20},"4.602472",".;1.18;.;0.61;.;.;1.19;.",".;.;.;.;.;.;2.73;.","0.999999;0.999995;0.999993",".;-6.32;-6.92;-6.52;.;.;-6.32;-6.38",".;.;.;.;.;.;1.0;.",".;0.003;0.007;0.004;.;.;0.004;0.004","0.837;0.837;.;0.83;0.831;0.831;0.822;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","371,0","0","371","0/1","482,82","0.1454","564",null,"chr2:71075561:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1395"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NANP","chr20:25616524","NANP(D50H)",null,null,"sequence conflict (In Ref. 1; BAB85055. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp50His","c.148G>C","MODERATE","50/248",2,{"$nulls":5},"5","154","113","108","76","149","102","0","0","0","0.1176",{"$nulls":20},"3.274113","3.24","2.395","0.934423","-2.21","0.938","0.007","0.332",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","146,0","0","146","0/1","99,14","0.1239","113",null,"chr20:25616524:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1184"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NCKAP5","chr2:132860551","NCKAP5(R250G)",null,null,"coiled-coil region , splice variant (In isoform 4. ), splice variant (In isoform 3. ), sequence variant (In dbSNP:rs58963837. NCKAP5(R250Q))",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg250Gly","c.748C>G","MODERATE","250/1909",12,{"$nulls":5},"5","367","427","252","280","347","387","0","0","0","0.124",{"$nulls":20},"4.062489","2.56;2.56;0.59;0.59","1.795;.;.;1.795","0.972618","-5.26;-5.26;-5.03;-5.03","0.989;.;.;1.0","0.002;0.002;0.005;0.005","0.739;0.626;0.716;0.71",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","354,0","0","354","0/1","359,51","0.1244","410",null,"chr2:132860551:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1286"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NCKAP5","chr2:132860551","NCKAP5(R250G)",null,null,"coiled-coil region , splice variant (In isoform 4. ), splice variant (In isoform 3. ), sequence variant (In dbSNP:rs58963837. NCKAP5(R250Q))",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg250Gly","c.748C>G","MODERATE","250/1909",12,{"$nulls":5},"5","367","460","252","310","346","430","0","0","0","0.0674",{"$nulls":20},"4.062489","2.56;2.56;0.59;0.59","1.795;.;.;1.795","0.972618","-5.26;-5.26;-5.03;-5.03","0.989;.;.;1.0","0.002;0.002;0.005;0.005","0.739;0.626;0.716;0.71",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","353,0","0","353","0/1","428,30","0.0655","458",null,"chr2:132860551:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0645"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NDUFC2","chr11:78073100","NDUFC2(F69fs)",null,null,"transmembrane region (Helical ), splice variant (In isoform 4. )",{"$nulls":3},58,"PASS","Loss Of Function","rs747914168",-1,null,"FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.; ","mitocarta",{"$nulls":3},"p.Phe69fs","c.207delT","HIGH","69/119",2,{"$nulls":5},"1",{"$nulls":15},"(NDUFC2-KCTD14|ENSG00000259112|1|1.00),(NDUFC2|ENSG00000151366|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","65,0","0","65","0/1","53,3","0.0536","56",null,"chr11:78073100:CA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0536"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NEK7","chr1:198319512","NEK7(A300G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Protein kinase which plays an important role in mitotic cell cycle progression. Required for microtubule nucleation activity of the centrosome, robust mitotic spindle formation and cytokinesis. Phosphorylates RPS6KB1. {ECO:0000269|PubMed:17101132, ECO:0000269|PubMed:17586473, ECO:0000269|PubMed:19414596}.; ",{"$nulls":4},"p.Ala300Gly","c.899C>G","MODERATE","300/302",10,{"$nulls":5},"4","441","669","284","446","411","599","0","0","0","0.212",{"$nulls":20},"2.331761","-0.6","0.895","0.999923","-0.81","0.031","0.032","0.244;0.384",{"$nulls":3},"Unknown",-1,{"$nulls":4},"NIMA-related kinases share high amino acid sequence identity with the gene product of the Aspergillus nidulans 'never in mitosis A' gene, which controls initiation of mitosis.[supplied by OMIM, Jul 2002].  ",null,null,"0/0","434,0","0","434","0/1","503,157","0.2379","660",null,"chr1:198319512:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2466"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NEK7","chr1:198319512","NEK7(A300G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Protein kinase which plays an important role in mitotic cell cycle progression. Required for microtubule nucleation activity of the centrosome, robust mitotic spindle formation and cytokinesis. Phosphorylates RPS6KB1. {ECO:0000269|PubMed:17101132, ECO:0000269|PubMed:17586473, ECO:0000269|PubMed:19414596}.; ",{"$nulls":4},"p.Ala300Gly","c.899C>G","MODERATE","300/302",10,{"$nulls":5},"4","441","622","284","419","411","574","0","0","0","0.1307",{"$nulls":20},"2.331761","-0.6","0.895","0.999923","-0.81","0.031","0.032","0.244;0.384",{"$nulls":3},"Unknown",-1,{"$nulls":4},"NIMA-related kinases share high amino acid sequence identity with the gene product of the Aspergillus nidulans 'never in mitosis A' gene, which controls initiation of mitosis.[supplied by OMIM, Jul 2002].  ",null,null,"0/0","434,0","0","434","0/1","523,89","0.1454","612",null,"chr1:198319512:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1217"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NET1","chr10:5455049","NET1(Q376Q)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase. May be involved in activation of the SAPK/JNK pathway Stimulates genotoxic stress-induced RHOB activity in breast cancer cells leading to their cell death. {ECO:0000269|PubMed:21373644}.; ",{"$nulls":5},"c.1128G>A","HIGH",null,10,{"$nulls":5},"5","188","374","129","236","176","328","0","0","0","0.2256",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","180,0","0","180","0/1","263,89","0.2528","352",null,"chr10:5455049:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2415"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NET1","chr10:5455049","NET1(Q376Q)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase. May be involved in activation of the SAPK/JNK pathway Stimulates genotoxic stress-induced RHOB activity in breast cancer cells leading to their cell death. {ECO:0000269|PubMed:21373644}.; ",{"$nulls":5},"c.1128G>A","HIGH",null,10,{"$nulls":5},"5","188","273","129","177","173","239","0","0","0","0.1339",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","183,0","0","183","0/1","223,37","0.1423","260",null,"chr10:5455049:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1356"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NFIA","chr1:61088620","NFIA(H212N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Brain malformations with or without urinary tract defects (BRMUTD) [MIM:613735]: A syndrome characterized by corpus callosum hypoplasia or agenesis, hydrocephalus or ventricular enlargement, developmental delay, and urinary tract defects. {ECO:0000269|PubMed:24462883, ECO:0000269|PubMed:27081522}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Recognizes and binds the palindromic sequence 5'- TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.; ",{"$nulls":4},"p.His212Asn","c.634C>A","MODERATE","212/554",3,{"$nulls":5},"4","307","301","221","222","286","273","0","0","0","0.1502",{"$nulls":20},"3.834285","-2.57;.;-2.57;-2.57;-2.57;-2.57;-2.57;-2.57;-2.57",".;.;.;.;2.56;2.56;.;.;.","1","-5.83;.;-5.83;-5.83;-5.83;-6.12;-6.3;-5.69;-6.06","0.925;.;.;.;0.925;0.769;.;.;.","0.0;.;0.0;0.0;0.0;0.0;0.0;0.0;0.001","0.9;.;0.878;0.909;0.908;0.869;0.831;0.868;0.877",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4478940","0/0","298,0","0","298","0/1","250,42","0.1438","292",null,"chr1:61088620:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1532"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NFIA","chr1:61088620","NFIA(H212N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Brain malformations with or without urinary tract defects (BRMUTD) [MIM:613735]: A syndrome characterized by corpus callosum hypoplasia or agenesis, hydrocephalus or ventricular enlargement, developmental delay, and urinary tract defects. {ECO:0000269|PubMed:24462883, ECO:0000269|PubMed:27081522}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Recognizes and binds the palindromic sequence 5'- TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.; ",{"$nulls":4},"p.His212Asn","c.634C>A","MODERATE","212/554",3,{"$nulls":5},"4","307","327","221","225","286","304","0","0","0","0.0724",{"$nulls":20},"3.834285","-2.57;.;-2.57;-2.57;-2.57;-2.57;-2.57;-2.57;-2.57",".;.;.;.;2.56;2.56;.;.;.","1","-5.83;.;-5.83;-5.83;-5.83;-6.12;-6.3;-5.69;-6.06","0.925;.;.;.;0.925;0.769;.;.;.","0.0;.;0.0;0.0;0.0;0.0;0.0;0.0;0.001","0.9;.;0.878;0.909;0.908;0.869;0.831;0.868;0.877",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4478940","0/0","299,0","0","299","0/1","288,26","0.0828","314",null,"chr1:61088620:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.08"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NKD1","chr16:50625572","NKD1(T152A)",null,null,"domain (EF-hand ), calcium-binding region , region of interest (Interaction with DVL1, DVL2 and DVL3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell autonomous antagonist of the canonical Wnt signaling pathway. May activate a second Wnt signaling pathway that controls planar cell polarity. {ECO:0000269|PubMed:11752446, ECO:0000269|PubMed:15687260, ECO:0000269|PubMed:16567647}.; ","level2",{"$nulls":3},"p.Thr152Ala","c.454A>G","MODERATE","152/470",6,{"$nulls":5},"5","475","509","337","358","416","456","0","0","0","0.1491",{"$nulls":20},"4.033237","5.6","2.805","1","-5.0","1.0","0.002","0.987",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kWNT",{"$nulls":3},"0/0","459,0","0","459","0/1","417,70","0.1437","487",null,"chr16:50625572:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1369"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NKD1","chr16:50625572","NKD1(T152A)",null,null,"domain (EF-hand ), calcium-binding region , region of interest (Interaction with DVL1, DVL2 and DVL3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell autonomous antagonist of the canonical Wnt signaling pathway. May activate a second Wnt signaling pathway that controls planar cell polarity. {ECO:0000269|PubMed:11752446, ECO:0000269|PubMed:15687260, ECO:0000269|PubMed:16567647}.; ","level2",{"$nulls":3},"p.Thr152Ala","c.454A>G","MODERATE","152/470",6,{"$nulls":5},"5","475","622","337","416","416","544","0","0","0","0.057",{"$nulls":20},"4.033237","5.6","2.805","1","-5.0","1.0","0.002","0.987",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kWNT",{"$nulls":3},"0/0","455,0","0","455","0/1","561,38","0.0634","599",null,"chr16:50625572:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0553"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NLGN1","chr3:173807714","NLGN1(M176I)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and probably mediates its effects by recruiting and clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses. Required to maintain wakefulness quality and normal synchrony of cerebral cortex activity during wakefulness and sleep. {ECO:0000250|UniProtKB:Q99K10}.; ",{"$nulls":4},"p.Met176Ile","c.528G>T","MODERATE","176/823",3,1,{"$nulls":4},"4","289","412","222","330","230","346","0.0035","0.0035","0","0.2543",{"$nulls":20},"3.505552","-0.6",null,"1","-3.33;-3.33;-3.26","0.998;0.998;.","0.117;0.117;0.216","0.803;0.845;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN280925","0/0","268,1","0.0037","269","0/1","300,94","0.2386","394",null,"chr3:173807714:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2515"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NLGN1","chr3:173807714","NLGN1(M176I)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and probably mediates its effects by recruiting and clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. In vitro, triggers the de novo formation of presynaptic structures. May be involved in specification of excitatory synapses. Required to maintain wakefulness quality and normal synchrony of cerebral cortex activity during wakefulness and sleep. {ECO:0000250|UniProtKB:Q99K10}.; ",{"$nulls":4},"p.Met176Ile","c.528G>T","MODERATE","176/823",3,1,{"$nulls":4},"4","289","366","222","300","229","297","0.0035","0.0035","0","0.1246",{"$nulls":20},"3.505552","-0.6",null,"1","-3.33;-3.33;-3.26","0.998;0.998;.","0.117;0.117;0.216","0.803;0.845;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN280925","0/0","268,1","0.0037","269","0/1","309,40","0.1146","349",null,"chr3:173807714:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1267"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NLRP6","chr11:280600","NLRP6(G289D)",null,null,"domain (NACHT )",{"$nulls":3},255,"PASS","Missense","rs1273363575",-1,null,"FUNCTION: As the sensor component of the NLRP6 inflammasome, plays a crucial role in innate immunity and inflammation. In response to pathogens and other damage-associated signals, initiates the formation of the inflammasome polymeric complex, made of NLRP6, PYCARD and CASP1 (and possibly CASP4 and CASP5). Recruitment of proCASP1 to the inflammasome promotes its activation and CASP1- catalyzed IL1B and IL18 maturation and secretion in the extracellular milieu. The precise NLRP6 activation stimulus has not been identified yet (By similarity) (PubMed:12387869). Essential for gut mucosal self-renewal and proliferation. Maintains intestinal homeostasis and a healthy intestinal microbiota. This function is, at least partially, mediated by IL18, and not IL1B, produced by nonhematopoietic cells. Influences intestinal barrier function and microbial homeostasis through the regulation of goblet cell mucus secretion. Acts by promoting autophagy in goblet cells, an essential step for mucus granule exocytosis. Its role in goblet cell physiology is inflammasome- dependent, but IL1B- and IL18-independent. During systemic bacterial infections, may negatively regulate inflammatory signaling and inhibit the influx of monocytes and neutrophils to the circulation and to the peritoneum. May promote peripheral nerve recovery following injury via an inflammasome-independent mechanism (By similarity). {ECO:0000250|UniProtKB:Q91WS2, ECO:0000250|UniProtKB:Q96P20, ECO:0000269|PubMed:12387869}.; ",{"$nulls":4},"p.Gly289Asp","c.866G>A","MODERATE","289/892",4,{"$nulls":5},"5","135","85","107","65","117","70","0","0","0","0.2429",{"$nulls":20},"0.695401","-1.23",null,"1","2.87",".;0.224","1.0","0.078",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","137,0","0","137","0/1","64,18","0.2195","82",null,"chr11:280600:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2154"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NLRP6","chr11:280600","NLRP6(G289D)",null,null,"domain (NACHT )",{"$nulls":3},255,"PASS","Missense","rs1273363575",-1,null,"FUNCTION: As the sensor component of the NLRP6 inflammasome, plays a crucial role in innate immunity and inflammation. In response to pathogens and other damage-associated signals, initiates the formation of the inflammasome polymeric complex, made of NLRP6, PYCARD and CASP1 (and possibly CASP4 and CASP5). Recruitment of proCASP1 to the inflammasome promotes its activation and CASP1- catalyzed IL1B and IL18 maturation and secretion in the extracellular milieu. The precise NLRP6 activation stimulus has not been identified yet (By similarity) (PubMed:12387869). Essential for gut mucosal self-renewal and proliferation. Maintains intestinal homeostasis and a healthy intestinal microbiota. This function is, at least partially, mediated by IL18, and not IL1B, produced by nonhematopoietic cells. Influences intestinal barrier function and microbial homeostasis through the regulation of goblet cell mucus secretion. Acts by promoting autophagy in goblet cells, an essential step for mucus granule exocytosis. Its role in goblet cell physiology is inflammasome- dependent, but IL1B- and IL18-independent. During systemic bacterial infections, may negatively regulate inflammatory signaling and inhibit the influx of monocytes and neutrophils to the circulation and to the peritoneum. May promote peripheral nerve recovery following injury via an inflammasome-independent mechanism (By similarity). {ECO:0000250|UniProtKB:Q91WS2, ECO:0000250|UniProtKB:Q96P20, ECO:0000269|PubMed:12387869}.; ",{"$nulls":4},"p.Gly289Asp","c.866G>A","MODERATE","289/892",4,{"$nulls":5},"5","135","127","107","96","117","105","0","0","0","0.0667",{"$nulls":20},"0.695401","-1.23",null,"1","2.87",".;0.224","1.0","0.078",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","137,0","0","137","0/1","119,7","0.0556","126",null,"chr11:280600:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NOBOX","chr7:144401174","NOBOX(R239Q)",{"$nulls":6},255,"PASS","Missense","rs769903404",0.0007096,null,"FUNCTION: Transcription factor which may play a role in oogenesis. Binds preferentially to the DNA sequences 5'-TAATTG-3', 5'-TAGTTG- 3' and 5'-TAATTA-3'. {ECO:0000269|PubMed:25514101, ECO:0000269|PubMed:27798098}.; ",{"$nulls":4},"p.Arg239Gln","c.716G>A","MODERATE","239/691",4,2,{"$nulls":4},"2","683","846",{"$nulls":4},"0.0015","0.0015",{"$nulls":22},"2.618348",".;-2.94;-3.19",".;1.495;1.495","0.999549",".;-1.11;-1.08",".;.;0.999",".;0.003;0.031",".;0.216;0.212",{"$nulls":3},"ExAC_EAS_AF",0.0007096,"AD","Premature ovarian failure 5","Endocrine; Obstetric",null,"This homeobox gene encodes a transcription factor that is thought to play a role in oogenesis. In mice, it is essential for folliculogenesis and regulation of oocyte-specific genes. Defects in this gene result in premature ovarian failure type 5.[provided by RefSeq, May 2011].  ",null,"C1969060","0/0","661,1","0.0015","662","0/1","714,98","0.1207","812",null,"chr7:144401174:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NOTCH1","chr9:136496223","NOTCH1(E2506*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Aortic valve disease 1 (AOVD1) [MIM:109730]: A common defect in the aortic valve in which two rather than three leaflets are present. It is often associated with aortic valve calcification, stenosis and insufficiency. In extreme cases, the blood flow may be so restricted that the left ventricle fails to grow, resulting in hypoplastic left heart syndrome. {ECO:0000269|PubMed:16025100}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adams-Oliver syndrome 5 (AOS5) [MIM:616028]: A form of Adams-Oliver syndrome, a disorder characterized by the congenital absence of skin (aplasia cutis congenita) in combination with transverse limb defects. Aplasia cutis congenita can be located anywhere on the body, but in the vast majority of the cases, it is present on the posterior parietal region where it is often associated with an underlying defect of the parietal bones. Limb abnormalities are typically limb truncation defects affecting the distal phalanges or entire digits (true ectrodactyly). Only rarely, metatarsals/metacarpals or more proximal limb structures are also affected. Apart from transverse limb defects, syndactyly, most commonly of second and third toes, can also be observed. The clinical features are highly variable and can also include cardiovascular malformations, brain abnormalities and vascular defects such as cutis marmorata and dilated scalp veins. {ECO:0000269|PubMed:25132448}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Functions as a receptor for membrane-bound ligands Jagged-1 (JAG1), Jagged-2 (JAG2) and Delta-1 (DLL1) to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus. Affects the implementation of differentiation, proliferation and apoptotic programs. Involved in angiogenesis; negatively regulates endothelial cell proliferation and migration and angiogenic sprouting. Involved in the maturation of both CD4(+) and CD8(+) cells in the thymus. Important for follicular differentiation and possibly cell fate selection within the follicle. During cerebellar development, functions as a receptor for neuronal DNER and is involved in the differentiation of Bergmann glia. Represses neuronal and myogenic differentiation. May play an essential role in postimplantation development, probably in some aspect of cell specification and/or differentiation. May be involved in mesoderm development, somite formation and neurogenesis. May enhance HIF1A function by sequestering HIF1AN away from HIF1A. Required for the THBS4 function in regulating protective astrogenesis from the subventricular zone (SVZ) niche after injury. Involved in determination of left/right symmetry by modulating the balance between motile and immotile (sensory) cilia at the left-right organiser (LRO). {ECO:0000269|PubMed:20616313}.; ","gedi|foundationOne|illumina|ion|level2",{"$nulls":3},"p.Glu2506*","c.7516G>T","HIGH","2506/2555",34,2,{"$nulls":4},"5","440","656","329","447","398","581","0","0","0","0.642",{"$nulls":20},"9.273501",null,null,"1",{"$nulls":3},"0.625",{"$nulls":3},"Unknown",-1,"AD","Aortic valve disease","Cardiovascular; Dermatologic; Musculoskeletal","COSMIC,kNOTCH,vp53",null,null,"C4014970| C3887892","0/0","430,0","0","430","0/1","225,419","0.6506","644",null,"chr9:136496223:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.6331"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NOTCH1","chr9:136496223","NOTCH1(E2506*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Aortic valve disease 1 (AOVD1) [MIM:109730]: A common defect in the aortic valve in which two rather than three leaflets are present. It is often associated with aortic valve calcification, stenosis and insufficiency. In extreme cases, the blood flow may be so restricted that the left ventricle fails to grow, resulting in hypoplastic left heart syndrome. {ECO:0000269|PubMed:16025100}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adams-Oliver syndrome 5 (AOS5) [MIM:616028]: A form of Adams-Oliver syndrome, a disorder characterized by the congenital absence of skin (aplasia cutis congenita) in combination with transverse limb defects. Aplasia cutis congenita can be located anywhere on the body, but in the vast majority of the cases, it is present on the posterior parietal region where it is often associated with an underlying defect of the parietal bones. Limb abnormalities are typically limb truncation defects affecting the distal phalanges or entire digits (true ectrodactyly). Only rarely, metatarsals/metacarpals or more proximal limb structures are also affected. Apart from transverse limb defects, syndactyly, most commonly of second and third toes, can also be observed. The clinical features are highly variable and can also include cardiovascular malformations, brain abnormalities and vascular defects such as cutis marmorata and dilated scalp veins. {ECO:0000269|PubMed:25132448}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Functions as a receptor for membrane-bound ligands Jagged-1 (JAG1), Jagged-2 (JAG2) and Delta-1 (DLL1) to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus. Affects the implementation of differentiation, proliferation and apoptotic programs. Involved in angiogenesis; negatively regulates endothelial cell proliferation and migration and angiogenic sprouting. Involved in the maturation of both CD4(+) and CD8(+) cells in the thymus. Important for follicular differentiation and possibly cell fate selection within the follicle. During cerebellar development, functions as a receptor for neuronal DNER and is involved in the differentiation of Bergmann glia. Represses neuronal and myogenic differentiation. May play an essential role in postimplantation development, probably in some aspect of cell specification and/or differentiation. May be involved in mesoderm development, somite formation and neurogenesis. May enhance HIF1A function by sequestering HIF1AN away from HIF1A. Required for the THBS4 function in regulating protective astrogenesis from the subventricular zone (SVZ) niche after injury. Involved in determination of left/right symmetry by modulating the balance between motile and immotile (sensory) cilia at the left-right organiser (LRO). {ECO:0000269|PubMed:20616313}.; ","gedi|foundationOne|illumina|ion|level2",{"$nulls":3},"p.Glu2506*","c.7516G>T","HIGH","2506/2555",34,2,{"$nulls":4},"5","440","678","329","473","395","585","0","0","0","0.3949",{"$nulls":20},"9.273501",null,null,"1",{"$nulls":3},"0.625",{"$nulls":3},"Unknown",-1,"AD","Aortic valve disease","Cardiovascular; Dermatologic; Musculoskeletal","COSMIC,kNOTCH,vp53",null,null,"C4014970| C3887892","0/0","435,0","0","435","0/1","398,269","0.4033","667",null,"chr9:136496223:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3911"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NPIPB4","chr16:21837216","NPIPB4(R391S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg391Ser","c.1171C>A","MODERATE","391/1138",7,{"$nulls":5},"1",{"$nulls":30},"0.975703","2.29;.",null,null,"0.32;-0.09","0.983;.","0.173;0.612","0.124;0.174",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,3","0.0163","189","0/1","111,118","0.5153","231",null,"chr16:21837216:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NR0B1","chrX:30304821","NR0B1(V391L)",null,null,"domain (NR LBD ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Adrenal hypoplasia, congenital (AHC) [MIM:300200]: A disorder of adrenal gland development characterized by absence of the permanent zone of the adrenal cortex, structural disorganization of the adrenal glands, adrenal insufficiency and profound hormonal deficiencies. AHC patients manifest primary adrenal failure usually in early infancy, and hypogonadotropic hypogonadism leading to absent or incomplete sexual maturation. AHC can be inherited in an X-linked or autosomal recessive pattern. {ECO:0000269|PubMed:10323730, ECO:0000269|PubMed:10341858, ECO:0000269|PubMed:10675358, ECO:0000269|PubMed:10848616, ECO:0000269|PubMed:11113848, ECO:0000269|PubMed:11443184, ECO:0000269|PubMed:11748852, ECO:0000269|PubMed:11788621, ECO:0000269|PubMed:12629128, ECO:0000269|PubMed:15800903, ECO:0000269|PubMed:7990958, ECO:0000269|PubMed:9003500, ECO:0000269|PubMed:9063431, ECO:0000269|PubMed:9360549, ECO:0000269|PubMed:9415399, ECO:0000269|PubMed:9529340}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: 46,XY sex reversal 2 (SRXY2) [MIM:300018]: A condition characterized by male-to-female sex reversal in the presence of a normal 46,XY karyotype. {ECO:0000269|PubMed:9486644}. Note=The disease is caused by mutations affecting the gene represented in this entry. XY individuals with a duplication of part of the short arm of the X chromosome and an intact SRY gene develop as females. The single X chromosome in these individuals does not undergo X- chromosome inactivation; therefore, these individuals presumably carry 2 active copies of genes, including the NR0B1 gene, in the duplicated region. Individuals with deletion of this region develop as males. Genes within the dosage-sensitive sex reversal region are, therefore, not essential for testis development, but, when present in a double dose, interfere with testis formation.; ","FUNCTION: Orphan nuclear receptor. Component of a cascade required for the development of the hypothalamic-pituitary-adrenal-gonadal axis. Acts as a coregulatory protein that inhibits the transcriptional activity of other nuclear receptors through heterodimeric interactions. May also have a role in the development of the embryo and in the maintenance of embryonic stem cell pluripotency (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Val391Leu","c.1171G>C","MODERATE","391/470",2,{"$nulls":5},"5","243","245","165","178","227","231","0","0","0","0.1818",{"$nulls":20},"0.085538","-4.97","-0.915","0.565246","-0.47","0.001","1.0","0.05",{"$nulls":3},"Unknown",-1,"XL","Adrenal hypoplasia, congenital; 46,XY sex reversal 2 ","Endocrine; Genitourinary; Obstetric; Oncologic",{"$nulls":3},"C0342482| C1848296","0/0","240,0","0","240","0/1","194,48","0.1983","242",null,"chrX:30304821:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2022"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","NR0B1","chrX:30304821","NR0B1(V391L)",null,null,"domain (NR LBD ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Adrenal hypoplasia, congenital (AHC) [MIM:300200]: A disorder of adrenal gland development characterized by absence of the permanent zone of the adrenal cortex, structural disorganization of the adrenal glands, adrenal insufficiency and profound hormonal deficiencies. AHC patients manifest primary adrenal failure usually in early infancy, and hypogonadotropic hypogonadism leading to absent or incomplete sexual maturation. AHC can be inherited in an X-linked or autosomal recessive pattern. {ECO:0000269|PubMed:10323730, ECO:0000269|PubMed:10341858, ECO:0000269|PubMed:10675358, ECO:0000269|PubMed:10848616, ECO:0000269|PubMed:11113848, ECO:0000269|PubMed:11443184, ECO:0000269|PubMed:11748852, ECO:0000269|PubMed:11788621, ECO:0000269|PubMed:12629128, ECO:0000269|PubMed:15800903, ECO:0000269|PubMed:7990958, ECO:0000269|PubMed:9003500, ECO:0000269|PubMed:9063431, ECO:0000269|PubMed:9360549, ECO:0000269|PubMed:9415399, ECO:0000269|PubMed:9529340}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: 46,XY sex reversal 2 (SRXY2) [MIM:300018]: A condition characterized by male-to-female sex reversal in the presence of a normal 46,XY karyotype. {ECO:0000269|PubMed:9486644}. Note=The disease is caused by mutations affecting the gene represented in this entry. XY individuals with a duplication of part of the short arm of the X chromosome and an intact SRY gene develop as females. The single X chromosome in these individuals does not undergo X- chromosome inactivation; therefore, these individuals presumably carry 2 active copies of genes, including the NR0B1 gene, in the duplicated region. Individuals with deletion of this region develop as males. Genes within the dosage-sensitive sex reversal region are, therefore, not essential for testis development, but, when present in a double dose, interfere with testis formation.; ","FUNCTION: Orphan nuclear receptor. Component of a cascade required for the development of the hypothalamic-pituitary-adrenal-gonadal axis. Acts as a coregulatory protein that inhibits the transcriptional activity of other nuclear receptors through heterodimeric interactions. May also have a role in the development of the embryo and in the maintenance of embryonic stem cell pluripotency (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Val391Leu","c.1171G>C","MODERATE","391/470",2,{"$nulls":5},"5","243","308","165","211","227","289","0","0","0","0.1176",{"$nulls":20},"0.085538","-4.97","-0.915","0.565246","-0.47","0.001","1.0","0.05",{"$nulls":3},"Unknown",-1,"XL","Adrenal hypoplasia, congenital; 46,XY sex reversal 2 ","Endocrine; Genitourinary; Obstetric; Oncologic",{"$nulls":3},"C0342482| C1848296","0/0","240,0","0","240","0/1","263,43","0.1405","306",null,"chrX:30304821:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1517"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NUP85","chr17:75208578","NUP85(P29A)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance (PubMed:12718872). As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP96/Nup98 and NUP153 to the nucleus (PubMed:12718872). The Nup107-160 complex seems to be required for spindle assembly during mitosis (PubMed:16807356). NUP85 is required for membrane clustering of CCL2-activated CCR2 (PubMed:15995708). Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol 3-kinase-Rac-lammellipodium protrusion cascade (PubMed:15995708). {ECO:0000269|PubMed:12718872, ECO:0000269|PubMed:15995708, ECO:0000269|PubMed:16807356}.; ",{"$nulls":4},"p.Pro29Ala","c.85C>G","MODERATE","29/656",2,{"$nulls":5},"5","306","233","201","142","259","201","0","0","0","0.0945",{"$nulls":20},"2.004298",null,".;2.215;.","0.99998;0.99998;1;1;1",".;-3.18;.",".;0.816;.",".;0.135;.",".;0.552;0.589",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748545","0/0","295,0","0","295","0/1","203,26","0.1135","229",null,"chr17:75208578:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1268"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","NXPE3","chr3:101821701","NXPE3(K476R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys476Arg","c.1427A>G","MODERATE","476/559",8,{"$nulls":5},"4","869","1078","681","804","779","926","0","0","0","0.1361",{"$nulls":20},"1.8344200000000002","2.27","0.905","0.746667","-0.79","0.121","0.451","0.151;0.156;0.143",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","849,0","0","849","0/1","912,146","0.138","1058",null,"chr3:101821701:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1405"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OGDHL","chr10:49752140","OGDHL(R196H)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs141198160",0.0005781,null,null,"mitocarta",{"$nulls":3},"p.Arg196His","c.587G>A","MODERATE","196/1010",5,{"$nulls":5},"4","442","675","329","485","371","558","0.0023","0.0023","0","0.0771",{"$nulls":20},"4.07254","2.54","1.715;.","1","-4.2;-4.28","1.0","0.046;0.036","0.724;0.691",{"$nulls":3},"ExAC_AFR_AF",0.0005781,{"$nulls":7},"0/0","428,1","0.0023","429","0/1","602,50","0.0767","652",null,"chr10:49752140:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0742"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR10J1","chr1:159440698","OR10J1(A314S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ala314Ser","c.940G>T","MODERATE","314/320",1,{"$nulls":5},"4","281","363","212","267","262","334","0","0","0","0.2126",{"$nulls":20},"1.757547",null,".;1.165;.","1",null,".;0.096;.",{"$nulls":5},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","279,0","0","279","0/1","276,75","0.2137","351",null,"chr1:159440698:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2172"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR10J1","chr1:159440698","OR10J1(A314S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ala314Ser","c.940G>T","MODERATE","314/320",1,{"$nulls":5},"4","281","342","212","243","262","327","0","0","0","0.1193",{"$nulls":20},"1.757547",null,".;1.165;.","1",null,".;0.096;.",{"$nulls":5},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","278,0","0","278","0/1","285,43","0.1311","328",null,"chr1:159440698:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1235"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR4C3","chr11:48325210","OR4C3(N90K)",{"$nulls":6},255,"PASS","Missense","rs1364872133",-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn90Lys","c.270C>A","MODERATE","90/329",1,{"$nulls":5},"5","507","547","456","468","394","375","0","0","0","0.1867",{"$nulls":20},"0.992887",null,"1.765;.","1",null,"0.076;.",{"$nulls":5},"Unknown",-1,{"$nulls":7},"0/0","503,0","0","503","0/1","447,96","0.1768","543",null,"chr11:48325210:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1581"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR4C3","chr11:48325210","OR4C3(N90K)",{"$nulls":6},255,"PASS","Missense","rs1364872133",-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn90Lys","c.270C>A","MODERATE","90/329",1,{"$nulls":5},"4",null,null,"456","491","392","386",null,null,"0","0.0803",{"$nulls":20},"0.992887",null,"1.765;.","1",null,"0.076;.",{"$nulls":5},"Unknown",-1,{"$nulls":7},"0/0","503,0","0","503","0/1","502,44","0.0806","546",null,"chr11:48325210:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0794"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR4D9","chr11:59515145","OR4D9(A78V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ala78Val","c.233C>T","MODERATE","78/314",1,{"$nulls":5},"5","642","650","489","487","555","558","0","0","0","0.1434",{"$nulls":20},"-0.455606",".;.;4.45","-0.975","1",".;.;-1.22","0.003",".;.;0.347",".;.;0.061",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","633,0","0","633","0/1","538,99","0.1554","637",null,"chr11:59515145:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1458"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR4D9","chr11:59515145","OR4D9(A78V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ala78Val","c.233C>T","MODERATE","78/314",1,{"$nulls":5},"4","642","762","489","556","556","670","0","0","0","0.0791",{"$nulls":20},"-0.455606",".;.;4.45","-0.975","1",".;.;-1.22","0.003",".;.;0.347",".;.;0.061",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","633,0","0","633","0/1","690,61","0.0812","751",null,"chr11:59515145:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0737"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR4K1","chr14:19935891","OR4K1(N75K)",{"$nulls":6},255,"PASS","Missense","rs769564787",0.0001922,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn75Lys","c.225C>A","MODERATE","75/311",1,1,{"$nulls":4},"4","951","1085","740","830","798","928","0","0","0","0.1606",{"$nulls":20},"1.7434020000000001",".;.;7.58","1.28","0.999994",".;.;-1.31","0.045",".;.;0.001",".;.;0.401",{"$nulls":3},"ExAC_AFR_AF",0.0001922,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","918,0","0","918","0/1","887,164","0.156","1051",null,"chr14:19935891:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1578"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR4K1","chr14:19935891","OR4K1(N75K)",{"$nulls":6},255,"PASS","Missense","rs769564787",0.0001922,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn75Lys","c.225C>A","MODERATE","75/311",1,1,{"$nulls":4},"4","951","1076","740","814","799","914","0","0","0","0.0635",{"$nulls":20},"1.7434020000000001",".;.;7.58","1.28","0.999994",".;.;-1.31","0.045",".;.;0.001",".;.;0.401",{"$nulls":3},"ExAC_AFR_AF",0.0001922,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","912,0","0","912","0/1","973,65","0.0626","1038",null,"chr14:19935891:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0639"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR4K13","chr14:20033999","OR4K13(C254S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Cys254Ser","c.760T>A","MODERATE","254/304",1,{"$nulls":5},"5","120","153","102","120","108","134","0","0","0","0.1567",{"$nulls":20},"1.6556579999999999",".;.;8.75","1.805","1",".;.;-8.53","0.164",".;.;0.031",".;.;0.364",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","117,0","0","117","0/1","125,27","0.1776","152",null,"chr14:20033999:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1833"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR4K13","chr14:20033999","OR4K13(C254S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Cys254Ser","c.760T>A","MODERATE","254/304",1,{"$nulls":5},"5","120","180","102","136","108","161","0","0","0","0.0559",{"$nulls":20},"1.6556579999999999",".;.;8.75","1.805","1",".;.;-8.53","0.164",".;.;0.031",".;.;0.364",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","117,0","0","117","0/1","168,11","0.0615","179",null,"chr14:20033999:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0735"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR4N5","chr14:20144076","OR4N5(L114H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Leu114His","c.341T>A","MODERATE","114/308",1,{"$nulls":5},"4","576","692","482","580","486","618","0","0","0","0.3366",{"$nulls":20},"2.8914590000000002",".;6.33","4.57","0.971169",".;-4.12","1.0",".;0.0",".;0.668",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","560,1","0.0018","561","0/1","454,232","0.3382","686",null,"chr14:20144076:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3483"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR4N5","chr14:20144076","OR4N5(L114H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Leu114His","c.341T>A","MODERATE","114/308",1,{"$nulls":5},"4","576","698","482","579","488","601","0","0","0","0.1614",{"$nulls":20},"2.8914590000000002",".;6.33","4.57","0.971169",".;-4.12","1.0",".;0.0",".;0.668",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","562,0","0","562","0/1","588,108","0.1552","696",null,"chr14:20144076:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1589"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR51S1","chr11:4848542","OR51S1(F223V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Phe223Val","c.667T>G","MODERATE","223/323",1,1,{"$nulls":4},"5","194","195","151","159","161","166","0","0","0","0.241",{"$nulls":20},"1.308582","1.27","0.78","0.999998;1","0.33","0.002","0.168","0.079",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","192,0","0","192","0/1","149,46","0.2359","195",null,"chr11:4848542:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.239"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR51S1","chr11:4848542","OR51S1(F223V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Phe223Val","c.667T>G","MODERATE","223/323",1,1,{"$nulls":4},"5","194","219","151","172","162","192","0","0","0","0.0938",{"$nulls":20},"1.308582","1.27","0.78","0.999998;1","0.33","0.002","0.168","0.079",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","192,0","0","192","0/1","197,20","0.0922","217",null,"chr11:4848542:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.093"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR51S1","chr11:4848734","OR51S1(R159G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Arg159Gly","c.475C>G","MODERATE","159/323",1,{"$nulls":5},"5","189","209","151","158","168","186","0","0","0","0.2204",{"$nulls":20},"2.264605","-0.59","2.18","0.999998;1","-6.02","0.922",null,"0.355",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","184,0","0","184","0/1","157,48","0.2341","205",null,"chr11:4848734:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2215"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","OR51S1","chr11:4848734","OR51S1(R159G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Arg159Gly","c.475C>G","MODERATE","159/323",1,{"$nulls":5},"5","189","228","151","169","168","196","0","0","0","0.1173",{"$nulls":20},"2.264605","-0.59","2.18","0.999998;1","-6.02","0.922",null,"0.355",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","184,0","0","184","0/1","204,24","0.1053","228",null,"chr11:4848734:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1006"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","OR5A2","chr11:59422947","OR5A2(V3L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Val3Leu","c.7G>T","MODERATE","3/324",1,{"$nulls":5},"4","215","250","165","166","207","230","0","0","0","0.1261",{"$nulls":20},"0.047137","9.85;.;.","0.385","1","-0.62;.;.","0.005","0.306;.;.","0.05;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","215,0","0","215","0/1","211,34","0.1388","245",null,"chr11:59422947:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1145"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PARD3B","chr2:205301474","PARD3B(Sequence Feature)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,null,"FUNCTION: Putative adapter protein involved in asymmetrical cell division and cell polarization processes. May play a role in the formation of epithelial tight junctions.; ",{"$nulls":5},"c.2403T>A","MODERATE",null,18,{"$nulls":5},"2","354","517",{"$nulls":4},"0.0028","0.0028",{"$nulls":33},"Unknown",-1,{"$nulls":7},"0/0","344,1","0.0029","345","0/1","453,53","0.1047","506",null,"chr2:205301474:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PARP15","chr3:122626975","PARP15(R463fs)",null,null,"domain (Macro 2 )",{"$nulls":3},255,"PASS","Loss Of Function","rs750794681",-1,null,"FUNCTION: Possesses ADP-ribosyltransferase activity (PubMed:16061477, PubMed:25635049). Transcriptional repressor (PubMed:16061477). {ECO:0000269|PubMed:16061477, ECO:0000269|PubMed:25635049}.; ",{"$nulls":4},"p.Arg463fs","c.1387dupA","HIGH","463/678",9,{"$nulls":5},"5","279","240","190","162","243","225","0","0","0","0.1556",{"$nulls":5},"(PARP15|ENSG00000173200|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","237,0","0","237","0/1","165,39","0.1912","204",null,"chr3:122626975:G:GA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1605"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PARP15","chr3:122626975","PARP15(R463fs)",null,null,"domain (Macro 2 )",{"$nulls":3},42.7217,"PASS","Loss Of Function","rs750794681",-1,null,"FUNCTION: Possesses ADP-ribosyltransferase activity (PubMed:16061477, PubMed:25635049). Transcriptional repressor (PubMed:16061477). {ECO:0000269|PubMed:16061477, ECO:0000269|PubMed:25635049}.; ",{"$nulls":4},"p.Arg463fs","c.1387dupA","HIGH","463/678",9,{"$nulls":5},"3",null,null,"190","168",{"$nulls":11},"(PARP15|ENSG00000173200|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","243,0","0","243","0/1","231,14","0.0571","245",null,"chr3:122626975:G:GA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0655"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PCDHB14","chr5:141225163","PCDHB14(D553A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Asp553Ala","c.1658A>C","MODERATE","553/798",1,{"$nulls":5},"4","186","192","161","166","163","77","0","0","0","0.1818",{"$nulls":20},"3.6776109999999997","3.91;.","3.485;.","0.999309","-7.46;.","1.0;.","0.0;.","0.793;0.849",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","186,0","0","186","0/1","162,30","0.1562","192",null,"chr5:141225163:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1566"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PCDHB14","chr5:141225163","PCDHB14(D553A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Asp553Ala","c.1658A>C","MODERATE","553/798",1,{"$nulls":5},"3",null,null,"161","179","158","68",null,null,"0","0.1765",{"$nulls":20},"3.6776109999999997","3.91;.","3.485;.","0.999309","-7.46;.","1.0;.","0.0;.","0.793;0.849",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","186,0","0","186","0/1","194,24","0.1101","218",null,"chr5:141225163:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1061"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PCF11","chr11:83169424","PCF11(R1030T)",null,null,"compositionally biased region (Gly-rich )","modified-residue:Dimethylated_arginine","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Component of pre-mRNA cleavage complex II.; ",{"$nulls":4},"p.Arg1030Thr","c.3089G>C","MODERATE","1030/1555",8,{"$nulls":5},"5","589","628","482","502","466","507","0","0","0","0.1854",{"$nulls":20},"3.180618","1.81","2.085","0.977969","-1.26","0.259",null,"0.818",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","578,0","0","578","0/1","500,109","0.179","609",null,"chr11:83169424:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1813"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PCF11","chr11:83169424","PCF11(R1030T)",null,null,"compositionally biased region (Gly-rich )","modified-residue:Dimethylated_arginine","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Component of pre-mRNA cleavage complex II.; ",{"$nulls":4},"p.Arg1030Thr","c.3089G>C","MODERATE","1030/1555",8,{"$nulls":5},"5","589","707","482","565","467","545","0","0","0","0.0679",{"$nulls":20},"3.180618","1.81","2.085","0.977969","-1.26","0.259",null,"0.818",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","580,0","0","580","0/1","645,45","0.0652","690",null,"chr11:83169424:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.069"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PELI1","chr2:64096266","PELI1(L183F)",null,null,"domain (FHA; atypical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. Involved in the TLR and IL-1 signaling pathways via interaction with the complex containing IRAK kinases and TRAF6. Mediates 'Lys-63'-linked polyubiquitination of IRAK1 allowing subsequent NF-kappa-B activation (PubMed:12496252, PubMed:17675297). Mediates 'Lys-48'- linked polyubiquitination of RIPK3 leading to its subsequent proteasome-dependent degradation; preferentially recognizes and mediates the degradation of the 'Thr-182' phosphorylated form of RIPK3 (PubMed:29883609). Negatively regulates necroptosis by reducing RIPK3 expression (PubMed:29883609). Mediates 'Lys-63'- linked ubiquitination of RIPK1 (PubMed:29883609). {ECO:0000269|PubMed:12496252, ECO:0000269|PubMed:17675297, ECO:0000269|PubMed:29883609}.; ",{"$nulls":4},"p.Leu183Phe","c.549G>C","MODERATE","183/418",6,{"$nulls":5},"5","604","654","429","484","498","523","0","0","0","0.1281",{"$nulls":20},"2.36964","0.07","3.07","0.999717","-3.82","1.0","0.001","0.88",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","576,0","0","576","0/1","545,81","0.1294","626",null,"chr2:64096266:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1219"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PELI1","chr2:64096266","PELI1(L183F)",null,null,"domain (FHA; atypical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. Involved in the TLR and IL-1 signaling pathways via interaction with the complex containing IRAK kinases and TRAF6. Mediates 'Lys-63'-linked polyubiquitination of IRAK1 allowing subsequent NF-kappa-B activation (PubMed:12496252, PubMed:17675297). Mediates 'Lys-48'- linked polyubiquitination of RIPK3 leading to its subsequent proteasome-dependent degradation; preferentially recognizes and mediates the degradation of the 'Thr-182' phosphorylated form of RIPK3 (PubMed:29883609). Negatively regulates necroptosis by reducing RIPK3 expression (PubMed:29883609). Mediates 'Lys-63'- linked ubiquitination of RIPK1 (PubMed:29883609). {ECO:0000269|PubMed:12496252, ECO:0000269|PubMed:17675297, ECO:0000269|PubMed:29883609}.; ",{"$nulls":4},"p.Leu183Phe","c.549G>C","MODERATE","183/418",6,{"$nulls":5},"5","604","691","429","498","497","563","0","0","0","0.0533",{"$nulls":20},"2.36964","0.07","3.07","0.999717","-3.82","1.0","0.001","0.88",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","568,0","0","568","0/1","635,36","0.0537","671",null,"chr2:64096266:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0522"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PGRMC2","chr4:128287739","PGRMC2(E42K)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for steroids. {ECO:0000305}.; ",{"$nulls":4},"p.Glu42Lys","c.124G>A","MODERATE","42/247",1,{"$nulls":5},"4","302","286","197","186","251","243","0","0","0","0.1317",{"$nulls":20},"3.775402",".;-1.03;-1.09",".;1.1;.","0.945968;0.708395",".;-0.53;-0.57",".;0.976;.",".;0.107;0.024","0.163;0.169;0.164",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","269,0","0","269","0/1","237,32","0.119","269",null,"chr4:128287739:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1344"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PGRMC2","chr4:128287739","PGRMC2(E42K)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for steroids. {ECO:0000305}.; ",{"$nulls":4},"p.Glu42Lys","c.124G>A","MODERATE","42/247",1,{"$nulls":5},"4","302","360","197","232","249","284","0","0","0","0.088",{"$nulls":20},"3.775402",".;-1.03;-1.09",".;1.1;.","0.945968;0.708395",".;-0.53;-0.57",".;0.976;.",".;0.107;0.024","0.163;0.169;0.164",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","267,0","0","267","0/1","291,30","0.0935","321",null,"chr4:128287739:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0862"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PHC2","chr1:33330085","PHC2(D711N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility.; ",{"$nulls":4},"p.Asp711Asn","c.2131G>A","MODERATE","711/858",12,{"$nulls":5},"5","473","545","345","414","394","451","0","0","0","0.1175",{"$nulls":20},"4.192892",".;.;0.99;1.57",".;.;.;1.355","0.998929",".;-1.54;-1.5;-1.29",".;.;.;0.999",".;0.049;0.092;0.035","0.259;0.198;0.224;0.243",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","438,0","0","438","0/1","456,59","0.1146","515",null,"chr1:33330085:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1063"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PHC2","chr1:33330085","PHC2(D711N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility.; ",{"$nulls":4},"p.Asp711Asn","c.2131G>A","MODERATE","711/858",12,{"$nulls":5},"5","473","588","345","434","394","495","0","0","0","0.0727",{"$nulls":20},"4.192892",".;.;0.99;1.57",".;.;.;1.355","0.998929",".;-1.54;-1.5;-1.29",".;.;.;0.999",".;0.049;0.092;0.035","0.259;0.198;0.224;0.243",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","443,0","0","443","0/1","525,34","0.0608","559",null,"chr1:33330085:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0599"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PHC3","chr3:170128743","PHC3(P577S)",null,null,"compositionally biased region (Pro-rich ), splice variant (In isoform 5 and isoform 6. ), splice variant (In isoform 4. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility. {ECO:0000269|PubMed:12167701}.; ",{"$nulls":4},"p.Pro577Ser","c.1729C>T","MODERATE","577/995",8,{"$nulls":5},"5","233","239","175","186","187","202","0","0","0","0.104",{"$nulls":20},"3.902265","1.16;1.04;.",".;2.085;.","1","-3.27;-3.27;-2.89","1.0","0.002;0.002;0.0","0.696;0.699;0.661",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","225,0","0","225","0/1","207,29","0.1229","236",null,"chr3:170128743:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1129"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PHC3","chr3:170128743","PHC3(P577S)",null,null,"compositionally biased region (Pro-rich ), splice variant (In isoform 5 and isoform 6. ), splice variant (In isoform 4. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility. {ECO:0000269|PubMed:12167701}.; ",{"$nulls":4},"p.Pro577Ser","c.1729C>T","MODERATE","577/995",8,{"$nulls":5},"5","233","268","175","217","189","217","0","0","0","0.0645",{"$nulls":20},"3.902265","1.16;1.04;.",".;2.085;.","1","-3.27;-3.27;-2.89","1.0","0.002;0.002;0.0","0.696;0.699;0.661",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","225,0","0","225","0/1","245,18","0.0684","263",null,"chr3:170128743:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0737"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PHF2","chr9:93676710","PHF2(P983_A984insPSTTP)",null,null,"compositionally biased region (Ser/Thr-rich )",{"$nulls":3},162,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA. {ECO:0000269|PubMed:20129925, ECO:0000269|PubMed:21167174, ECO:0000269|PubMed:21532585}.; ",{"$nulls":4},"p.Pro983_Ala984insProSerThrThrPro","c.2949_2950insCCCTCTACCACCCCT","MODERATE","984/1096",21,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":4},"This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","129,0","0","140","0/1","109,22","0.1538","143",null,"chr9:93676710:A:ACCCTCTACCACCCCT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1538"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PHKG2","chr16:30753513","PHKG2(D171A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glycogen storage disease 9C (GSD9C) [MIM:613027]: A metabolic disorder manifesting in infancy with hepatomegaly, growth retardation, hypotonia, liver dysfunction, and elevated plasma aminotransferases and lipids. These symptoms improve with age in most cases; however, some patients may develop hepatic fibrosis or cirrhosis. {ECO:0000269|PubMed:12930917, ECO:0000269|PubMed:8896567, ECO:0000269|PubMed:9245685}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalytic subunit of the phosphorylase b kinase (PHK), which mediates the neural and hormonal regulation of glycogen breakdown (glycogenolysis) by phosphorylating and thereby activating glycogen phosphorylase. May regulate glycogeneolysis in the testis. In vitro, phosphorylates PYGM (By similarity). {ECO:0000250, ECO:0000269|PubMed:10487978}.; ",{"$nulls":4},"p.Asp171Ala","c.512A>C","MODERATE","171/410",6,{"$nulls":5},"5","225","181","154","128","206","159","0.0044","0.0044","0","0.1132",{"$nulls":20},"4.216701","-3.15","4.345;.;4.345;.;.","1","-7.95;-8.0;-7.81;-7.95;-7.95","1.0;.;1.0;.;.","0.0","0.902;.;0.901;0.904;.",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease IXc","Biochemical; Gastrointestinal; Musculoskeletal; Neurologic",{"$nulls":3},"C2751643","0/0","220,1","0.0045","221","0/1","156,21","0.1186","177",null,"chr16:30753513:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1094"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PIF1","chr15:64821189","PIF1(Q355L)",null,null,"region of interest (Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity ), splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of both mitochondrial and nuclear genome stability. Efficiently unwinds G-quadruplex (G4) DNA structures and forked RNA-DNA hybrids. Resolves G4 structures, preventing replication pausing and double-strand breaks (DSBs) at G4 motifs. Involved in the maintenance of telomeric DNA. Inhibits telomere elongation, de novo telomere formation and telomere addition to DSBs via catalytic inhibition of telomerase. Reduces the processivity of telomerase by displacing active telomerase from DNA ends. Releases telomerase by unwinding the short telomerase RNA/telomeric DNA hybrid that is the intermediate in the telomerase reaction. Possesses an intrinsic strand annealing activity. {ECO:0000255|HAMAP-Rule:MF_03176, ECO:0000269|PubMed:16522649, ECO:0000269|PubMed:17172855, ECO:0000269|PubMed:17827721, ECO:0000269|PubMed:18835853, ECO:0000269|PubMed:19700773, ECO:0000269|PubMed:20524933, ECO:0000269|PubMed:23657261}.; ",{"$nulls":4},"p.Gln355Leu","c.1064A>T","MODERATE","355/707",6,{"$nulls":5},"5","626","387","482","291","540","327","0","0","0","0.1498",{"$nulls":20},"3.049588","-1.1","1.25","0.999819","-3.69","0.833;.;0.833","0.117;0.051;0.117","0.297;0.339;0.298",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","597,0","0","597","0/1","303,60","0.1653","363",null,"chr15:64821189:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1718"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PIF1","chr15:64821189","PIF1(Q355L)",null,null,"region of interest (Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity ), splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of both mitochondrial and nuclear genome stability. Efficiently unwinds G-quadruplex (G4) DNA structures and forked RNA-DNA hybrids. Resolves G4 structures, preventing replication pausing and double-strand breaks (DSBs) at G4 motifs. Involved in the maintenance of telomeric DNA. Inhibits telomere elongation, de novo telomere formation and telomere addition to DSBs via catalytic inhibition of telomerase. Reduces the processivity of telomerase by displacing active telomerase from DNA ends. Releases telomerase by unwinding the short telomerase RNA/telomeric DNA hybrid that is the intermediate in the telomerase reaction. Possesses an intrinsic strand annealing activity. {ECO:0000255|HAMAP-Rule:MF_03176, ECO:0000269|PubMed:16522649, ECO:0000269|PubMed:17172855, ECO:0000269|PubMed:17827721, ECO:0000269|PubMed:18835853, ECO:0000269|PubMed:19700773, ECO:0000269|PubMed:20524933, ECO:0000269|PubMed:23657261}.; ",{"$nulls":4},"p.Gln355Leu","c.1064A>T","MODERATE","355/707",6,{"$nulls":5},"5","626","520","482","405","540","457","0","0","0","0.105",{"$nulls":20},"3.049588","-1.1","1.25","0.999819","-3.69","0.833;.;0.833","0.117;0.051;0.117","0.297;0.339;0.298",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","610,0","0","610","0/1","462,50","0.0977","512",null,"chr15:64821189:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0988"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PITPNA","chr17:1553033","PITPNA(Q56H)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Catalyzes the transfer of PtdIns and phosphatidylcholine between membranes.; ",{"$nulls":5},"c.168G>C","HIGH",null,3,{"$nulls":5},"5","263","220","209","181","195","151","0","0","0","0.1457",{"$nulls":20},"3.307487","0.51","4.21;.;.","1","-4.26;-4.26;.","0.999;.;.","0.0;0.0;.","0.822;0.826;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","260,0","0","260","0/1","188,28","0.1296","216",null,"chr17:1553033:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1436"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PITPNA","chr17:1553033","PITPNA(Q56H)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Catalyzes the transfer of PtdIns and phosphatidylcholine between membranes.; ",{"$nulls":5},"c.168G>C","HIGH",null,3,{"$nulls":5},"5","263","265","209","209","195","197","0","0","0","0.0812",{"$nulls":20},"3.307487","0.51","4.21;.;.","1","-4.26;-4.26;.","0.999;.;.","0.0;0.0;.","0.822;0.826;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","260,0","0","260","0/1","243,19","0.0725","262",null,"chr17:1553033:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0718"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PLB1","chr2:28602873","PLB1(R909Q)",null,null,"topological domain (Extracellular ), repeat (3 ), region of interest (4 X 308-326 AA approximate repeats ), splice variant (In isoform 5. ), splice variant (In isoform 4. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs375629172",2.594706798131811E-4,null,"FUNCTION: Membrane-associated phospholipase. Exhibits a calcium- independent broad substrate specificity including phospholipase A2/lysophospholipase activity. Preferential hydrolysis at the sn-2 position of diacylphospholipids and diacyglycerol, whereas it shows no positional specificity toward triacylglycerol. Exhibits also esterase activity toward p-nitrophenyl. May act on the brush border membrane to facilitate the absorption of digested lipids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg909Gln","c.2726G>A","MODERATE","909/1458",39,{"$nulls":5},"5","440","324","295","219","409","282","0","0","0","0.1348",{"$nulls":20},"3.5801600000000002","1.98","3.045;.","0.706908;0.706908;1","-1.93;-2.07","0.999","0.196;0.168","0.82;0.802",{"$nulls":3},"ALSPAC_AF",2.594706798131811E-4,{"$nulls":7},"0/0","426,0","0","426","0/1","268,49","0.1546","317",null,"chr2:28602873:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1461"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PLB1","chr2:28602873","PLB1(R909Q)",null,null,"topological domain (Extracellular ), repeat (3 ), region of interest (4 X 308-326 AA approximate repeats ), splice variant (In isoform 5. ), splice variant (In isoform 4. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs375629172",2.594706798131811E-4,null,"FUNCTION: Membrane-associated phospholipase. Exhibits a calcium- independent broad substrate specificity including phospholipase A2/lysophospholipase activity. Preferential hydrolysis at the sn-2 position of diacylphospholipids and diacyglycerol, whereas it shows no positional specificity toward triacylglycerol. Exhibits also esterase activity toward p-nitrophenyl. May act on the brush border membrane to facilitate the absorption of digested lipids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg909Gln","c.2726G>A","MODERATE","909/1458",39,{"$nulls":5},"4","440","479",null,null,"408","432","0","0","0","0.0625",{"$nulls":20},"3.5801600000000002","1.98","3.045;.","0.706908;0.706908;1","-1.93;-2.07","0.999","0.196;0.168","0.82;0.802",{"$nulls":3},"ALSPAC_AF",2.594706798131811E-4,{"$nulls":7},"0/0","416,0","0","416","0/1","413,25","0.0571","438",null,"chr2:28602873:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PLEKHG2","chr19:39424948","PLEKHG2(P1272L)",{"$nulls":6},255,"PASS","Missense","rs1309530463",-1,"DISEASE: Leukodystrophy and acquired microcephaly with or without dystonia (LDAMD) [MIM:616763]: An autosomal recessive neurologic disorder characterized by profound mental retardation, dystonia, postnatal microcephaly, and white matter abnormalities consistent with leukodystrophy. {ECO:0000269|PubMed:26573021}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a transforming oncogene with exchange activity for CDC42 (By similarity). May be a guanine-nucleotide exchange factor (GEF) for RAC1 and CDC42. Activated by the binding to subunits beta and gamma of the heterotrimeric guanine nucleotide- binding protein (G protein) (PubMed:18045877). Involved in the regulation of actin polymerization (PubMed:26573021). {ECO:0000250|UniProtKB:Q6KAU7, ECO:0000269|PubMed:18045877, ECO:0000269|PubMed:26573021}.; ",{"$nulls":4},"p.Pro1272Leu","c.3815C>T","MODERATE","1272/1386",19,{"$nulls":5},"5","286","254","208","182","266","227","0","0","0","0.1322",{"$nulls":20},"2.784015","-0.2","1.04","0.999882;0.999882;1;1;1","-1.11","1.0","0.241","0.34",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225213","0/0","281,0","0","281","0/1","210,34","0.1393","244",null,"chr19:39424948:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1264"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PLEKHG2","chr19:39424948","PLEKHG2(P1272L)",{"$nulls":6},255,"PASS","Missense","rs1309530463",-1,"DISEASE: Leukodystrophy and acquired microcephaly with or without dystonia (LDAMD) [MIM:616763]: An autosomal recessive neurologic disorder characterized by profound mental retardation, dystonia, postnatal microcephaly, and white matter abnormalities consistent with leukodystrophy. {ECO:0000269|PubMed:26573021}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a transforming oncogene with exchange activity for CDC42 (By similarity). May be a guanine-nucleotide exchange factor (GEF) for RAC1 and CDC42. Activated by the binding to subunits beta and gamma of the heterotrimeric guanine nucleotide- binding protein (G protein) (PubMed:18045877). Involved in the regulation of actin polymerization (PubMed:26573021). {ECO:0000250|UniProtKB:Q6KAU7, ECO:0000269|PubMed:18045877, ECO:0000269|PubMed:26573021}.; ",{"$nulls":4},"p.Pro1272Leu","c.3815C>T","MODERATE","1272/1386",19,{"$nulls":5},"5","286","324","208","220","266","297","0","0","0","0.0909",{"$nulls":20},"2.784015","-0.2","1.04","0.999882;0.999882;1;1;1","-1.11","1.0","0.241","0.34",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225213","0/0","278,0","0","278","0/1","289,30","0.094","319",null,"chr19:39424948:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0864"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PLXNA4","chr7:132182128","PLXNA4(R1074H)",null,null,"topological domain (Extracellular ), domain (IPT/TIG 3 ), splice variant (In isoform 4. ), splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs770599241",6.059e-05,null,"FUNCTION: Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg1074His","c.3221G>A","MODERATE","1074/1894",17,{"$nulls":5},"5","600","733","427","510","539","652","0","0","0","0.1917",{"$nulls":20},"3.714159","-1.15","2.91","1","-2.46","0.973","0.05","0.833;0.828",{"$nulls":3},"ExAC_SAS_AF",6.059e-05,{"$nulls":7},"0/0","567,0","0","567","0/1","558,139","0.1994","697",null,"chr7:132182128:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1961"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PLXNA4","chr7:132182128","PLXNA4(R1074H)",null,null,"topological domain (Extracellular ), domain (IPT/TIG 3 ), splice variant (In isoform 4. ), splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs770599241",6.059e-05,null,"FUNCTION: Coreceptor for SEMA3A. Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance in the developing nervous system. Class 3 semaphorins bind to a complex composed of a neuropilin and a plexin. The plexin modulates the affinity of the complex for specific semaphorins, and its cytoplasmic domain is required for the activation of down-stream signaling events in the cytoplasm (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg1074His","c.3221G>A","MODERATE","1074/1894",17,{"$nulls":5},"5","600","685","427","485","541","589","0","0","0","0.1341",{"$nulls":20},"3.714159","-1.15","2.91","1","-2.46","0.973","0.05","0.833;0.828",{"$nulls":3},"ExAC_SAS_AF",6.059e-05,{"$nulls":7},"0/0","562,0","0","562","0/1","562,85","0.1314","647",null,"chr7:132182128:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1299"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PLXNB3","chrX:153777348","PLXNB3(E1713K)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. {ECO:0000269|PubMed:15218527, ECO:0000269|PubMed:20696765, ECO:0000269|PubMed:21706053}.; ",{"$nulls":4},"p.Glu1713Lys","c.5137G>A","MODERATE","1713/1932",31,{"$nulls":5},"5","632","488","481","369","507","378","0","0","0","0.2249",{"$nulls":20},"4.00927","1.88",".;3.135","1","-3.8",".;1.0","0.0","0.917;0.905",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the plexin family. It functions as a receptor for semaphorin 5A, and plays a role in axon guidance, invasive growth and cell migration. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].",null,null,"0/0","613,0","0","613","0/1","374,90","0.194","464",null,"chrX:153777348:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1843"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PLXNB3","chrX:153777348","PLXNB3(E1713K)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. {ECO:0000269|PubMed:15218527, ECO:0000269|PubMed:20696765, ECO:0000269|PubMed:21706053}.; ",{"$nulls":4},"p.Glu1713Lys","c.5137G>A","MODERATE","1713/1932",31,{"$nulls":5},"5","632","608","481","448","508","476","0","0","0","0.1155",{"$nulls":20},"4.00927","1.88",".;3.135","1","-3.8",".;1.0","0.0","0.917;0.905",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the plexin family. It functions as a receptor for semaphorin 5A, and plays a role in axon guidance, invasive growth and cell migration. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].",null,null,"0/0","615,0","0","615","0/1","532,62","0.1044","594",null,"chrX:153777348:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1027"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PODN","chr1:53077755","PODN(Q318P)",null,null,"repeat (LRR 10 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Negatively regulates cell proliferation and cell migration. {ECO:0000269|PubMed:15063725}.; ",{"$nulls":4},"p.Gln318Pro","c.953A>C","MODERATE","318/661",7,{"$nulls":5},"4","778","809","542","584","638","666","0","0","0","0.1411",{"$nulls":20},"3.9319319999999998","0.33;0.33;.;0.33",null,"0.999764;0.999684;0.999684","-4.23;-4.34;.;-4.46","0.996;0.997;0.997;0.973","0.056;0.012;.;0.011","0.911;0.92;0.92;0.925",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","712,0","0","712","0/1","637,113","0.1507","750",null,"chr1:53077755:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1524"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PODN","chr1:53077755","PODN(Q318P)",null,null,"repeat (LRR 10 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Negatively regulates cell proliferation and cell migration. {ECO:0000269|PubMed:15063725}.; ",{"$nulls":4},"p.Gln318Pro","c.953A>C","MODERATE","318/661",7,{"$nulls":5},"4","778","862","542","618","637","710","0","0","0","0.0662",{"$nulls":20},"3.9319319999999998","0.33;0.33;.;0.33",null,"0.999764;0.999684;0.999684","-4.23;-4.34;.;-4.46","0.996;0.997;0.997;0.973","0.056;0.012;.;0.011","0.911;0.92;0.92;0.925",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","732,0","0","732","0/1","774,54","0.0652","828",null,"chr1:53077755:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0744"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","POP1","chr8:98158096","POP1(V967A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Anauxetic dysplasia 2 (ANXD2) [MIM:617396]: An autosomal recessive spondyloepimetaphyseal dysplasia characterized by severe short stature of prenatal onset, very short adult height (less than 1 meter), hypodontia, midface hypoplasia, and mild intellectual disability. {ECO:0000269|PubMed:21455487, ECO:0000269|PubMed:27380734, ECO:0000269|PubMed:28067412}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP.; ",{"$nulls":4},"p.Val967Ala","c.2900T>C","MODERATE","967/1024",16,{"$nulls":5},"4","790","1771","583","1291","712","1566","0","0","0","0.0766",{"$nulls":20},"4.193288","2.5","3.07","0.999974","-3.53","1.0","0.003","0.832;0.881",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4479357","0/0","739,0","0","739","0/1","1563,126","0.0746","1689",null,"chr8:98158096:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0744"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","POR","chr7:75985614","POR(Y531fs)",null,null,"topological domain (Cytoplasmic ), strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Antley-Bixler syndrome, with genital anomalies and disordered steroidogenesis (ABS1) [MIM:201750]: A disease characterized by the association of Antley-Bixler syndrome with steroidogenesis defects and abnormal genitalia. Antley-Bixler syndrome is characterized by craniosynostosis, radiohumeral synostosis present from the perinatal period, midface hypoplasia, choanal stenosis or atresia, femoral bowing and multiple joint contractures. {ECO:0000269|PubMed:14758361, ECO:0000269|PubMed:15264278, ECO:0000269|PubMed:15483095}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Disordered steroidogenesis due to cytochrome P450 oxidoreductase deficiency (DISPORD) [MIM:613571]: A disorder resulting in a rare variant of congenital adrenal hyperplasia, with apparent combined P450C17 and P450C21 deficiency and accumulation of steroid metabolites. Affected girls are born with ambiguous genitalia, but their circulating androgens are low and virilization does not progress. Conversely, affected boys are sometimes born undermasculinized. Boys and girls can present with bone malformations, in some cases resembling the pattern seen in patients with Antley-Bixler syndrome. {ECO:0000269|PubMed:14758361, ECO:0000269|PubMed:15220035}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: This enzyme is required for electron transfer from NADP to cytochrome P450 in microsomes. It can also provide electron transfer to heme oxygenase and cytochrome B5. {ECO:0000255|HAMAP- Rule:MF_03212}.; ",{"$nulls":4},"p.Tyr531fs","c.1587_1591dupGGAGT","HIGH","531/724",12,{"$nulls":5},"4","718","759","501","549","616","700","0","0","0","0.12",{"$nulls":5},"(POR|ENSG00000127948|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Antley-Bixler syndrome; Disordered steroidogenesis due to cytochrome p450 oxidoreductase deficiency","Craniofacial; Endocrine; Genitourinary; Musculoskeletal; Neurologic",null,"This gene encodes an endoplasmic reticulum membrane oxidoreductase with an FAD-binding domain and a flavodoxin-like domain. The protein binds two cofactors, FAD and FMN, which allow it to donate electrons directly from NADPH to all microsomal P450 enzymes. Mutations in this gene have been associated with various diseases, including apparent combined P450C17 and P450C21 deficiency, amenorrhea and disordered steroidogenesis, congenital adrenal hyperplasia and Antley-Bixler syndrome. [provided by RefSeq, Jul 2008].  CCDS Note: This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primate species. This starting position is most commonly referred to in the literature, and the numbering system used to describe disease-associated mutations is based on this protein start. This includes data in the P450 oxidoreductase (POR) allele nomenclature locus-specific database, and the Human Gene Mutation Database (HGMD). This start codon is restricted to higher primate species, and it has a weak Kozak signal. However, it should be noted that an alternative downstream start codon, which has a strong Kozak signal and is much more widely conserved, is also present. The use of this downstream start codon would result in a protein that is 3 aa shorter at the N-terminus. Protein sequencing in PMID:2513880 indicates that this is the preferred start codon in vivo. It is therefore possible that the ribosome will initiate at the upstream start codon only a small fraction of the time (if at all), while leaky scanning will allow the downstream start codon to be used predominantly.  ",null,"C3150099| C2673964| C2936791","0/0","618,0","0","618","0/1","582,91","0.1352","673",null,"chr7:75985614:T:TGTGGA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1311"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","POR","chr7:75985614","POR(Y531fs)",null,null,"topological domain (Cytoplasmic ), strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Antley-Bixler syndrome, with genital anomalies and disordered steroidogenesis (ABS1) [MIM:201750]: A disease characterized by the association of Antley-Bixler syndrome with steroidogenesis defects and abnormal genitalia. Antley-Bixler syndrome is characterized by craniosynostosis, radiohumeral synostosis present from the perinatal period, midface hypoplasia, choanal stenosis or atresia, femoral bowing and multiple joint contractures. {ECO:0000269|PubMed:14758361, ECO:0000269|PubMed:15264278, ECO:0000269|PubMed:15483095}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Disordered steroidogenesis due to cytochrome P450 oxidoreductase deficiency (DISPORD) [MIM:613571]: A disorder resulting in a rare variant of congenital adrenal hyperplasia, with apparent combined P450C17 and P450C21 deficiency and accumulation of steroid metabolites. Affected girls are born with ambiguous genitalia, but their circulating androgens are low and virilization does not progress. Conversely, affected boys are sometimes born undermasculinized. Boys and girls can present with bone malformations, in some cases resembling the pattern seen in patients with Antley-Bixler syndrome. {ECO:0000269|PubMed:14758361, ECO:0000269|PubMed:15220035}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: This enzyme is required for electron transfer from NADP to cytochrome P450 in microsomes. It can also provide electron transfer to heme oxygenase and cytochrome B5. {ECO:0000255|HAMAP- Rule:MF_03212}.; ",{"$nulls":4},"p.Tyr531fs","c.1587_1591dupGGAGT","HIGH","531/724",12,{"$nulls":5},"3",null,null,"501","580","616","718",null,null,"0","0.0501",{"$nulls":5},"(POR|ENSG00000127948|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Antley-Bixler syndrome; Disordered steroidogenesis due to cytochrome p450 oxidoreductase deficiency","Craniofacial; Endocrine; Genitourinary; Musculoskeletal; Neurologic",null,"This gene encodes an endoplasmic reticulum membrane oxidoreductase with an FAD-binding domain and a flavodoxin-like domain. The protein binds two cofactors, FAD and FMN, which allow it to donate electrons directly from NADPH to all microsomal P450 enzymes. Mutations in this gene have been associated with various diseases, including apparent combined P450C17 and P450C21 deficiency, amenorrhea and disordered steroidogenesis, congenital adrenal hyperplasia and Antley-Bixler syndrome. [provided by RefSeq, Jul 2008].  CCDS Note: This CCDS representation uses the 5'-most in-frame start codon, which is conserved in higher primate species. This starting position is most commonly referred to in the literature, and the numbering system used to describe disease-associated mutations is based on this protein start. This includes data in the P450 oxidoreductase (POR) allele nomenclature locus-specific database, and the Human Gene Mutation Database (HGMD). This start codon is restricted to higher primate species, and it has a weak Kozak signal. However, it should be noted that an alternative downstream start codon, which has a strong Kozak signal and is much more widely conserved, is also present. The use of this downstream start codon would result in a protein that is 3 aa shorter at the N-terminus. Protein sequencing in PMID:2513880 indicates that this is the preferred start codon in vivo. It is therefore possible that the ribosome will initiate at the upstream start codon only a small fraction of the time (if at all), while leaky scanning will allow the downstream start codon to be used predominantly.  ",null,"C3150099| C2673964| C2936791","0/0","622,0","0","622","0/1","641,40","0.0587","681",null,"chr7:75985614:T:TGTGGA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0569"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","POSTN","chr13:37584053","POSTN(L387I)",null,null,"domain (FAS1 3 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Induces cell attachment and spreading and plays a role in cell adhesion (PubMed:12235007). Enhances incorporation of BMP1 in the fibronectin matrix of connective tissues, and subsequent proteolytic activation of lysyl oxidase LOX (By similarity). {ECO:0000250|UniProtKB:Q62009, ECO:0000269|PubMed:12235007}.; ",{"$nulls":4},"p.Leu387Ile","c.1159C>A","MODERATE","387/836",9,1,{"$nulls":4},"5","393","519","254","346","348","471","0.0025","0.0025","0","0.1444",{"$nulls":20},"3.621606","-2.99","2.7;.;2.7;2.7;2.7;2.7","0.980401","-1.07","0.999;.;.;0.975;.;0.97","0.194;0.188;0.172;0.185;0.19;0.197","0.472;0.461;0.484;0.431;0.478;0.473",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","370,1","0.0027","371","0/1","405,72","0.1509","477",null,"chr13:37584053:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1445"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","POSTN","chr13:37584053","POSTN(L387I)",null,null,"domain (FAS1 3 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Induces cell attachment and spreading and plays a role in cell adhesion (PubMed:12235007). Enhances incorporation of BMP1 in the fibronectin matrix of connective tissues, and subsequent proteolytic activation of lysyl oxidase LOX (By similarity). {ECO:0000250|UniProtKB:Q62009, ECO:0000269|PubMed:12235007}.; ",{"$nulls":4},"p.Leu387Ile","c.1159C>A","MODERATE","387/836",9,1,{"$nulls":4},"5","393","557","254","364","354","522","0.0025","0.0025","0","0.0536",{"$nulls":20},"3.621606","-2.99","2.7;.;2.7;2.7;2.7;2.7","0.980401","-1.07","0.999;.;.;0.975;.;0.97","0.194;0.188;0.172;0.185;0.19;0.197","0.472;0.461;0.484;0.431;0.478;0.473",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","371,1","0.0027","372","0/1","493,36","0.0681","529",null,"chr13:37584053:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0577"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","POTED","chr21:13610285","POTED(L20fs)",{"$nulls":6},94,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Leu20fs","c.57_68del<DELETE_NUC>insT","HIGH","20/584",1,{"$nulls":5},"1",{"$nulls":14},"13610508",{"$nulls":26},"Unknown",-1,{"$nulls":7},"0/0","67,0","0","67","0/1","78,8","0.1026","78",null,"chr21:13610285:<DELETE_NUC>:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1026"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PPL","chr16:4885825","PPL(P944S)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs1029398489",-1,null,"FUNCTION: Component of the cornified envelope of keratinocytes. May link the cornified envelope to desmosomes and intermediate filaments. May act as a localization signal in PKB/AKT-mediated signaling. {ECO:0000269|PubMed:9412476}.; ",{"$nulls":4},"p.Pro944Ser","c.2830C>T","MODERATE","944/1756",22,{"$nulls":5},"4","436","562","351","452","340","440","0","0","0","0.2045",{"$nulls":20},"3.319656","0.14;0.14;-0.1","2.98;.;.","1","-7.03;.;.","1.0;.;.","0.0;.;.","0.665;0.774;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","419,0","0","419","0/1","432,108","0.2","540",null,"chr16:4885825:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.208"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PPL","chr16:4885825","PPL(P944S)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs1029398489",-1,null,"FUNCTION: Component of the cornified envelope of keratinocytes. May link the cornified envelope to desmosomes and intermediate filaments. May act as a localization signal in PKB/AKT-mediated signaling. {ECO:0000269|PubMed:9412476}.; ",{"$nulls":4},"p.Pro944Ser","c.2830C>T","MODERATE","944/1756",22,{"$nulls":5},"4","436","590","351","458","343","468","0","0","0","0.1538",{"$nulls":20},"3.319656","0.14;0.14;-0.1","2.98;.;.","1","-7.03;.;.","1.0;.;.","0.0;.;.","0.665;0.774;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","418,0","0","418","0/1","482,83","0.1469","565",null,"chr16:4885825:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1376"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PPP1R9A","chr7:95284094","PPP1R9A(M1125L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to actin filaments (F-actin) and shows cross- linking activity. Binds along the sides of the F-actin. May be involved in neurite formation. Inhibits protein phosphatase 1- alpha activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met1125Leu","c.3373A>C","MODERATE","1125/1374",17,{"$nulls":5},"5","579","700","439","517","484","564","0","0","0","0.1188",{"$nulls":20},"1.4237060000000001","2.64;2.62;2.62;2.62",null,"1;1;0.997393;0.997393;0.998872;0.997393","-0.69;-0.86;-0.86;-0.82",null,"0.397;0.352;0.352;0.361","0.136;0.155;0.191;0.175",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is imprinted, and located in a cluster of imprinted genes on chromosome 7q12. This gene is transcribed in both neuronal and multiple embryonic tissues, and it is maternally expressed mainly in embryonic skeletal muscle tissues and biallelically expressed in other embryonic tissues. The protein encoded by this gene includes a PDZ domain and a sterile alpha motif (SAM). It is a regulatory subunit of protein phosphatase I, and controls actin cytoskeleton reorganization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009].",null,null,"0/0","559,0","0","559","0/1","602,80","0.1173","682",null,"chr7:95284094:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1083"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PPP1R9A","chr7:95284094","PPP1R9A(M1125L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to actin filaments (F-actin) and shows cross- linking activity. Binds along the sides of the F-actin. May be involved in neurite formation. Inhibits protein phosphatase 1- alpha activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met1125Leu","c.3373A>C","MODERATE","1125/1374",17,{"$nulls":5},"5","579","677","439","518","481","553","0","0","0","0.0615",{"$nulls":20},"1.4237060000000001","2.64;2.62;2.62;2.62",null,"1;1;0.997393;0.997393;0.998872;0.997393","-0.69;-0.86;-0.86;-0.82",null,"0.397;0.352;0.352;0.361","0.136;0.155;0.191;0.175",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is imprinted, and located in a cluster of imprinted genes on chromosome 7q12. This gene is transcribed in both neuronal and multiple embryonic tissues, and it is maternally expressed mainly in embryonic skeletal muscle tissues and biallelically expressed in other embryonic tissues. The protein encoded by this gene includes a PDZ domain and a sterile alpha motif (SAM). It is a regulatory subunit of protein phosphatase I, and controls actin cytoskeleton reorganization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009].",null,null,"0/0","561,0","0","561","0/1","615,40","0.0611","655",null,"chr7:95284094:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0656"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PRB3","chr12:11267567","PRB3(P228S)",{"$nulls":6},105,"PASS","Missense","rs12811811",-1,null,"FUNCTION: Acts as a receptor for the Gram-negative bacterium F.nucleatum. {ECO:0000269|PubMed:1894623}.; ",{"$nulls":4},"p.Pro228Ser","c.682C>T","MODERATE","228/351",3,3,{"$nulls":4},"1",{"$nulls":30},"0.171101","3.23",null,"0.999637","-0.88",null,null,"0.181",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","119,0","0","128","0/1","120,8","0.0571","140",null,"chr12:11267567:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0571"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PRLR","chr5:35084640","PRLR(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Multiple fibroadenomas of the breast (MFAB) [MIM:615554]: A benign breast disease marked by lobuloalveolar growth with abnormally high proliferation of the epithelium, and characterized by the presence of more than 3 fibroadenomas in one breast. Fibroadenomas are adenomas containing fibrous tissue. {ECO:0000269|PubMed:18779591}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hyperprolactinemia (HPRL) [MIM:615555]: A disorder characterized by increased levels of prolactin in the blood not associated with gestation or the puerperium. HPRL may result in infertility, hypogonadism, and galactorrhea. {ECO:0000269|PubMed:24195502}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: This is a receptor for the anterior pituitary hormone prolactin (PRL). Acts as a prosurvival factor for spermatozoa by inhibiting sperm capacitation through suppression of SRC kinase activation and stimulation of AKT. Isoform 4 is unable to transduce prolactin signaling. Isoform 6 is unable to transduce prolactin signaling. {ECO:0000269|PubMed:12580759, ECO:0000269|PubMed:20032052}.; ","level2",{"$nulls":4},"c.204-1G>T","HIGH",null,4,{"$nulls":5},"5","284","321","202","244","275","305","0","0","0","0.1377",{"$nulls":5},"(PRLR|ENSG00000113494|1|1.00)",{"$nulls":14},"3.800056",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Hyperprolactinemia; Multiple fibroadenomas of the breast","Endocrine; Oncologic","kJAK_STAT",null,null,"C0020514| C3809918","0/0","282,0","0","282","0/1","270,46","0.1456","316",null,"chr5:35084640:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1311"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PRLR","chr5:35084640","PRLR(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Multiple fibroadenomas of the breast (MFAB) [MIM:615554]: A benign breast disease marked by lobuloalveolar growth with abnormally high proliferation of the epithelium, and characterized by the presence of more than 3 fibroadenomas in one breast. Fibroadenomas are adenomas containing fibrous tissue. {ECO:0000269|PubMed:18779591}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hyperprolactinemia (HPRL) [MIM:615555]: A disorder characterized by increased levels of prolactin in the blood not associated with gestation or the puerperium. HPRL may result in infertility, hypogonadism, and galactorrhea. {ECO:0000269|PubMed:24195502}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: This is a receptor for the anterior pituitary hormone prolactin (PRL). Acts as a prosurvival factor for spermatozoa by inhibiting sperm capacitation through suppression of SRC kinase activation and stimulation of AKT. Isoform 4 is unable to transduce prolactin signaling. Isoform 6 is unable to transduce prolactin signaling. {ECO:0000269|PubMed:12580759, ECO:0000269|PubMed:20032052}.; ","level2",{"$nulls":4},"c.204-1G>T","HIGH",null,4,{"$nulls":5},"4","284","321",null,null,"275","307","0","0","0","0.0847",{"$nulls":5},"(PRLR|ENSG00000113494|1|1.00)",{"$nulls":14},"3.800056",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Hyperprolactinemia; Multiple fibroadenomas of the breast","Endocrine; Oncologic","kJAK_STAT",null,null,"C0020514| C3809918","0/0","283,0","0","283","0/1","285,31","0.0981","316",null,"chr5:35084640:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PRSS53","chr16:31084235","PRSS53(A509G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: In vitro can degrade the fibrinogen alpha chain of as well as pro-urokinase-type plasminogen activator. {ECO:0000269|PubMed:16566820}.; ",{"$nulls":4},"p.Ala509Gly","c.1526C>G","MODERATE","509/553",10,{"$nulls":5},"4","877","948","665","681","777","840","0","0","0","0.1095",{"$nulls":20},"1.555625","-2.08","-2.71","0.656718","3.01","0.02","1.0","0.304",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","859,0","0","859","0/1","816,106","0.115","922",null,"chr16:31084235:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.116"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PRSS53","chr16:31084235","PRSS53(A509G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: In vitro can degrade the fibrinogen alpha chain of as well as pro-urokinase-type plasminogen activator. {ECO:0000269|PubMed:16566820}.; ",{"$nulls":4},"p.Ala509Gly","c.1526C>G","MODERATE","509/553",10,{"$nulls":5},"4","877","1026","665","758","774","884","0","0","0","0.0633",{"$nulls":20},"1.555625","-2.08","-2.71","0.656718","3.01","0.02","1.0","0.304",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","847,0","0","847","0/1","928,67","0.0673","995",null,"chr16:31084235:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0646"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PSG5","chr19:43185027","PSG5(L62R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu62Arg","c.185T>G","MODERATE","62/428",2,{"$nulls":5},"4","994","1355","784","1042","827","1148","0","0","0","0.128",{"$nulls":20},"1.29575","-0.17","2.365;2.365;.;.;2.365;.","1","-3.23;-3.23;-3.78;.;-3.23;-3.2","0.925;0.925;0.98;.;0.925;.","0.042;0.042;0.048;.;0.042;0.04","0.34;0.304;0.526;0.324;0.337;0.344",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","963,0","0","963","0/1","1142,176","0.1335","1318",null,"chr19:43185027:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1209"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PSG5","chr19:43185027","PSG5(L62R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu62Arg","c.185T>G","MODERATE","62/428",2,{"$nulls":5},"4","994","1299","784","1015","826","1101","0","0","0","0.0654",{"$nulls":20},"1.29575","-0.17","2.365;2.365;.;.;2.365;.","1","-3.23;-3.23;-3.78;.;-3.23;-3.2","0.925;0.925;0.98;.;0.925;.","0.042;0.042;0.048;.;0.042;0.04","0.34;0.304;0.526;0.324;0.337;0.344",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","969,0","0","969","0/1","1171,79","0.0632","1250",null,"chr19:43185027:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0601"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PSMC3","chr11:47418940","PSMC3(M405I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. PSMC3 belongs to the heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitinated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. {ECO:0000269|PubMed:1317798}.; ",{"$nulls":4},"p.Met405Ile","c.1215G>C","MODERATE","405/439",12,{"$nulls":5},"5","247","164","180","117","215","144","0","0","0","0.1458",{"$nulls":20},"3.879579",".;-3.49;.;-3.49",".;2.095;2.095;.","1",".;-3.58;.;-3.58",".;0.997;0.997;0.738",".;0.023;.;0.022","0.882;0.856;0.828;0.813",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","240,0","0","240","0/1","138,26","0.1585","164",null,"chr11:47418940:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1453"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PSMC3","chr11:47418940","PSMC3(M405I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. PSMC3 belongs to the heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitinated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. {ECO:0000269|PubMed:1317798}.; ",{"$nulls":4},"p.Met405Ile","c.1215G>C","MODERATE","405/439",12,{"$nulls":5},"5","247","258","180","191","216","223","0","0","0","0.0673",{"$nulls":20},"3.879579",".;-3.49;.;-3.49",".;2.095;2.095;.","1",".;-3.58;.;-3.58",".;0.997;0.997;0.738",".;0.023;.;0.022","0.882;0.856;0.828;0.813",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","238,0","0","238","0/1","234,20","0.0787","254",null,"chr11:47418940:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0733"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PTCHD1","chrX:23392584","PTCHD1(E356K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for the development and function of the thalamic reticular nucleus (TRN), a part of the thalamus that is critical for thalamocortical transmission, generation of sleep rhythms, sensorimotor processing and attention. {ECO:0000250|UniProtKB:Q14B62}.; ",{"$nulls":4},"p.Glu356Lys","c.1066G>A","MODERATE","356/888",3,1,{"$nulls":4},"4","427","412","327","327","347","359","0","0","0","0.1393",{"$nulls":20},"2.846498","-1.88","1.955","0.999985","-0.99","0.145","0.106","0.696",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0795888| C1510586","0/0","407,0","0","407","0/1","346,50","0.1263","396",null,"chrX:23392584:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1346"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","PTCHD1","chrX:23392584","PTCHD1(E356K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for the development and function of the thalamic reticular nucleus (TRN), a part of the thalamus that is critical for thalamocortical transmission, generation of sleep rhythms, sensorimotor processing and attention. {ECO:0000250|UniProtKB:Q14B62}.; ",{"$nulls":4},"p.Glu356Lys","c.1066G>A","MODERATE","356/888",3,1,{"$nulls":4},"4","427","487","327","359","347","399","0","0","0","0.0902",{"$nulls":20},"2.846498","-1.88","1.955","0.999985","-0.99","0.145","0.106","0.696",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0795888| C1510586","0/0","407,0","0","407","0/1","434,41","0.0863","475",null,"chrX:23392584:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0724"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PTPN22","chr1:113859430","PTPN22(A40T)",null,null,"domain (Tyrosine-protein phosphatase ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Systemic lupus erythematosus (SLE) [MIM:152700]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269|PubMed:15273934}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Diabetes mellitus, insulin-dependent (IDDM) [MIM:222100]: A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:15004560}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Rheumatoid arthritis (RA) [MIM:180300]: An inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. {ECO:0000269|PubMed:15208781}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Vitiligo (VTLG) [MIM:193200]: A pigmentary disorder of the skin and mucous membranes. It is characterized by circumscribed depigmented macules and patches, commonly on extensor aspects of extremities, on the face or neck and in skin folds. Vitiligo is a progressive disorder in which some or all of the melanocytes in the affected skin are selectively destroyed. It is a multifactorial disorder with a complex etiology probably including autoimmune mechanisms, and is associated with an elevated risk of other autoimmune diseases. {ECO:0000269|PubMed:16015369}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as negative regulator of T-cell receptor (TCR) signaling by direct dephosphorylation of the Src family kinases LCK and FYN, ITAMs of the TCRz/CD3 complex, as well as ZAP70, VAV, VCP and other key signaling molecules (PubMed:16461343, PubMed:18056643). Associates with and probably dephosphorylates CBL. Dephosphorylates LCK at its activating 'Tyr-394' residue (PubMed:21719704). Dephosphorylates ZAP70 at its activating 'Tyr- 493' residue (PubMed:16461343). Dephosphorylates the immune system activator SKAP2 (PubMed:21719704). Positively regulates toll-like receptor (TLR)-induced type 1 interferon production (PubMed:23871208). Promotes host antiviral responses mediated by type 1 interferon (By similarity). Regulates NOD2-induced pro- inflammatory cytokine secretion and autophagy (PubMed:23991106). {ECO:0000250|UniProtKB:P29352, ECO:0000269|PubMed:16461343, ECO:0000269|PubMed:18056643, ECO:0000269|PubMed:19167335, ECO:0000269|PubMed:21719704, ECO:0000269|PubMed:23871208, ECO:0000269|PubMed:23991106}.; ",{"$nulls":4},"p.Ala40Thr","c.118G>A","MODERATE","40/807",2,{"$nulls":5},"5","510","541","347","343","478","490","0","0","0","0.102",{"$nulls":20},"1.491599","2.52;3.64;.;3.35;3.52;3.1","1.3;.;.;.;.;.","0.997518;0.997518;0.907467;0.997518;1;0.958243","0.62;0.2;.;0.2;0.2;0.4","0.001;.;.;.;0.001;.","1.0;0.624;.;0.442;0.432;1.0","0.092;0.093;0.1;0.097;0.083;0.097",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0024141| C0003873| C0011854","0/0","485,0","0","485","0/1","442,61","0.1213","503",null,"chr1:113859430:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1166"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","PTPN4","chr2:119960879","PTPN4(D736N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act at junctions between the membrane and the cytoskeleton.; ",{"$nulls":4},"p.Asp736Asn","c.2206G>A","MODERATE","736/926",23,1,{"$nulls":4},"5","651","830","450","561","575","724","0","0","0","0.1257",{"$nulls":20},"3.712241","2.02","3.35","1","-3.15","0.972","0.031","0.695",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","614,0","0","614","0/1","671,99","0.1286","770",null,"chr2:119960879:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1301"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","QSOX1","chr1:180154945","QSOX1(L19del)",null,null,"signal peptide ",{"$nulls":3},58,"PASS","Inframe Indel","rs775285773",-1,null,"FUNCTION: Catalyzes the oxidation of sulfhydryl groups in peptide and protein thiols to disulfides with the reduction of oxygen to hydrogen peroxide. May contribute to disulfide bond formation in a variety of secreted proteins. In fibroblasts, it may have tumor- suppressing capabilities being involved in growth regulation. {ECO:0000269|PubMed:10542195, ECO:0000269|PubMed:10708601, ECO:0000269|PubMed:12176051, ECO:0000269|PubMed:16806532, ECO:0000269|PubMed:17331072, ECO:0000269|PubMed:18393449}.; ",{"$nulls":4},"p.Leu19del","c.55_57delCTG","MODERATE","19/747",1,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","48,0","0","48","0/1","57,3","0.05","60",null,"chr1:180154945:CGCT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.05"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RAB30","chr11:82997226","RAB30(Q31E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). Required for maintaining the structural integrity of the Golgi apparatus, possibly by mediating interactions with cytoplasmic scaffolding proteins. {ECO:0000250, ECO:0000269|PubMed:22188167}.; ",{"$nulls":4},"p.Gln31Glu","c.91C>G","MODERATE","31/203",2,{"$nulls":5},"4","372","398","269","296","266","278","0","0","0","0.1403",{"$nulls":20},"3.7022310000000003",".;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.97;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98","-1.255;-1.255;-1.255;-1.255;-1.255;.;.;.;.;.;.;.;.;.","1;1;1;1;0.609896;1",".;-1.05;-1.4;-1.05;-1.05;-1.18;-1.32;-1.37;-1.4;-1.4;-1.47;-1.34;-1.42;-1.33","0.904;0.904;.;0.904;0.904;.;.;0.57;.;.;.;.;.;.",".;0.195;0.195;0.195;0.195;0.312;0.605;0.017;0.203;0.329;0.409;0.095;0.51;0.414","0.608;0.608;0.609;0.589;0.608;.;.;0.649;0.627;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","343,0","0","343","0/1","334,45","0.1187","379",null,"chr11:82997226:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1318"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RAB30","chr11:82997226","RAB30(Q31E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (By similarity). Required for maintaining the structural integrity of the Golgi apparatus, possibly by mediating interactions with cytoplasmic scaffolding proteins. {ECO:0000250, ECO:0000269|PubMed:22188167}.; ",{"$nulls":4},"p.Gln31Glu","c.91C>G","MODERATE","31/203",2,{"$nulls":5},"4","372","454","269","340","266","309","0","0","0","0.0809",{"$nulls":20},"3.7022310000000003",".;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.97;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98","-1.255;-1.255;-1.255;-1.255;-1.255;.;.;.;.;.;.;.;.;.","1;1;1;1;0.609896;1",".;-1.05;-1.4;-1.05;-1.05;-1.18;-1.32;-1.37;-1.4;-1.4;-1.47;-1.34;-1.42;-1.33","0.904;0.904;.;0.904;0.904;.;.;0.57;.;.;.;.;.;.",".;0.195;0.195;0.195;0.195;0.312;0.605;0.017;0.203;0.329;0.409;0.095;0.51;0.414","0.608;0.608;0.609;0.589;0.608;.;.;0.649;0.627;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","370,0","0","370","0/1","409,33","0.0747","442",null,"chr11:82997226:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0706"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RAD54B","chr8:94378294","RAD54B(H801N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in DNA repair and mitotic recombination. May play an active role in recombination processes in concert with other members of the RAD52 epistasis group. {ECO:0000269|PubMed:11782437, ECO:0000269|PubMed:11884632}.; ","level2",{"$nulls":3},"p.His801Asn","c.2401C>A","MODERATE","801/910",14,{"$nulls":5},"4","1037","2136","731","1507","778","1625","0","0","0","0.0954",{"$nulls":20},"2.372991","-0.87;.","1.24;.","1","-1.22;.","0.017;.","0.427;.","0.281;0.289",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kHOMOLOGOUS_RECOMBINATION",null,null,"C4721532| C1527249","0/0","951,0","0","951","0/1","1764,173","0.0893","1937",null,"chr8:94378294:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0869"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RAD54B","chr8:94378294","RAD54B(H801N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in DNA repair and mitotic recombination. May play an active role in recombination processes in concert with other members of the RAD52 epistasis group. {ECO:0000269|PubMed:11782437, ECO:0000269|PubMed:11884632}.; ","level2",{"$nulls":3},"p.His801Asn","c.2401C>A","MODERATE","801/910",14,{"$nulls":5},"3","1037","1601",null,null,"777","1204","0","0","0","0.0581",{"$nulls":20},"2.372991","-0.87;.","1.24;.","1","-1.22;.","0.017;.","0.427;.","0.281;0.289",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kHOMOLOGOUS_RECOMBINATION",null,null,"C4721532| C1527249","0/0","981,0","0","981","0/1","1443,78","0.0513","1521",null,"chr8:94378294:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RAE1","chr20:57354712","RAE1(D31H)",null,null,"sequence conflict (In Ref. 2; AAC28127. RAE1(D31G))",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in mitotic bipolar spindle formation (PubMed:17172455). Binds mRNA. May function in nucleocytoplasmic transport and in directly or indirectly attaching cytoplasmic mRNPs to the cytoskeleton. {ECO:0000269|PubMed:17172455}.; ",{"$nulls":4},"p.Asp31His","c.91G>C","MODERATE","31/437",3,{"$nulls":5},"5","592","1000","491","804","422","758","0","0","0","0.1187",{"$nulls":20},"5.096398","-0.57;-0.57;-0.34;1.61;1.61;-0.57;.","3.405;3.405;.;.;.;3.405;.","1","-5.75;-5.75;-5.87;-6.39;-6.39;-5.75;-6.19","1.0;1.0;1.0;.;.;1.0;.","0.001;0.001;0.0;0.001;0.001;0.001;0.002","0.919;0.916;0.92;.;.;0.922;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Mutations in the Schizosaccharomyces pombe Rae1 and Saccharomyces cerevisiae Gle2 genes have been shown to result in accumulation of poly(A)-containing mRNA in the nucleus, suggesting that the encoded proteins are involved in RNA export. The protein encoded by this gene is a homolog of yeast Rae1. It contains four WD40 motifs, and has been shown to localize to distinct foci in the nucleoplasm, to the nuclear rim, and to meshwork-like structures throughout the cytoplasm. This gene is thought to be involved in nucleocytoplasmic transport, and in directly or indirectly attaching cytoplasmic mRNPs to the cytoskeleton. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008].",null,null,"0/0","576,0","0","576","0/1","875,97","0.0998","972",null,"chr20:57354712:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0908"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RALBP1","chr18:9522433","RALBP1(D326G)",null,null,"domain (Rho-GAP ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Can activate specifically hydrolysis of GTP bound to RAC1 and CDC42, but not RALA. Mediates ATP-dependent transport of S-(2,4-dinitrophenyl)-glutathione (DNP-SG) and doxorubicin (DOX) and is the major ATP-dependent transporter of glutathione conjugates of electrophiles (GS-E) and DOX in erythrocytes. Can catalyze transport of glutathione conjugates and xenobiotics, and may contribute to the multidrug resistance phenomenon. Serves as a scaffold protein that brings together proteins forming an endocytotic complex during interphase and also with CDK1 to switch off endocytosis, One of its substrates would be EPN1/Epsin. {ECO:0000269|PubMed:11437348, ECO:0000269|PubMed:12775724, ECO:0000269|PubMed:7673236}.; ","level2",{"$nulls":3},"p.Asp326Gly","c.977A>G","MODERATE","326/655",4,{"$nulls":5},"5","491","505","398","407","432","254","0","0","0","0.1772",{"$nulls":20},"4.091601","2.22","0.665","1","-2.66","0.977","0.071","0.625;0.626",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER","RALBP1 plays a role in receptor-mediated endocytosis and is a downstream effector of the small GTP-binding protein RAL (see RALA; MIM 179550). Small G proteins, such as RAL, have GDP-bound inactive and GTP-bound active forms, which shift from the inactive to the active state through the action of RALGDS (MIM 601619), which in turn is activated by RAS (see HRAS; MIM 190020) (summary by Feig, 2003 [PubMed 12888294]).[supplied by OMIM, Nov 2010].  ",null,null,"0/0","486,0","0","486","0/1","427,74","0.1477","501",null,"chr18:9522433:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1474"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RALBP1","chr18:9522433","RALBP1(D326G)",null,null,"domain (Rho-GAP ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Can activate specifically hydrolysis of GTP bound to RAC1 and CDC42, but not RALA. Mediates ATP-dependent transport of S-(2,4-dinitrophenyl)-glutathione (DNP-SG) and doxorubicin (DOX) and is the major ATP-dependent transporter of glutathione conjugates of electrophiles (GS-E) and DOX in erythrocytes. Can catalyze transport of glutathione conjugates and xenobiotics, and may contribute to the multidrug resistance phenomenon. Serves as a scaffold protein that brings together proteins forming an endocytotic complex during interphase and also with CDK1 to switch off endocytosis, One of its substrates would be EPN1/Epsin. {ECO:0000269|PubMed:11437348, ECO:0000269|PubMed:12775724, ECO:0000269|PubMed:7673236}.; ","level2",{"$nulls":3},"p.Asp326Gly","c.977A>G","MODERATE","326/655",4,{"$nulls":5},"3",{"$nulls":4},"432","301",null,null,"0","0.0631",{"$nulls":20},"4.091601","2.22","0.665","1","-2.66","0.977","0.071","0.625;0.626",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER","RALBP1 plays a role in receptor-mediated endocytosis and is a downstream effector of the small GTP-binding protein RAL (see RALA; MIM 179550). Small G proteins, such as RAL, have GDP-bound inactive and GTP-bound active forms, which shift from the inactive to the active state through the action of RALGDS (MIM 601619), which in turn is activated by RAS (see HRAS; MIM 190020) (summary by Feig, 2003 [PubMed 12888294]).[supplied by OMIM, Nov 2010].  ",null,null,"0/0","489,0","0","489","0/1","520,30","0.0545","550",null,"chr18:9522433:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RCOR1","chr14:102593064","RCOR1(S60A)",null,null,"compositionally biased region (Ala-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development and controls hematopoietic differentiation. {ECO:0000269|PubMed:11171972, ECO:0000269|PubMed:11516394, ECO:0000269|PubMed:12032298, ECO:0000269|PubMed:12399542, ECO:0000269|PubMed:12493763, ECO:0000269|PubMed:16079794, ECO:0000269|PubMed:16140033}.; ",{"$nulls":4},"p.Ser60Ala","c.178T>G","MODERATE","60/485",1,{"$nulls":5},"4","56","41","45","36",null,null,"0","0",{"$nulls":22},"0.798607","1.01",null,"0.999993;0.999994",{"$nulls":3},"0.123",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein that is well-conserved, downregulated at birth, and with a specific role in determining neural cell differentiation. The encoded protein binds to the C-terminal domain of REST (repressor element-1 silencing transcription factor). [provided by RefSeq, Aug 2011].  ",null,null,"0/0","51,0","0","51","0/1","35,5","0.125","40",null,"chr14:102593064:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1389"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RECQL4","chr8:144512863","RECQL4(L913F)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Rothmund-Thomson syndrome (RTS) [MIM:268400]: Characterized by dermatological features such as atrophy, pigmentation, and telangiectasia and frequently accompanied by juvenile cataract, saddle nose, congenital bone defects, disturbances of hair growth, and hypogonadism. {ECO:0000269|PubMed:10552928}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: RAPADILINO syndrome (RAPADILINOS) [MIM:266280]: Disease characterized by radial and patellar aplasia or hypoplasia. {ECO:0000269|PubMed:12952869}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Baller-Gerold syndrome (BGS) [MIM:218600]: An autosomal recessive syndrome characterized by short stature, craniosynostosis, absent or hypoplastic radii, short and curved ulna, fused carpal bones and absent carpals, metacarpals and phalanges. Some patients manifest poikiloderma. Cases reported as Baller-Gerold syndrome have phenotypic overlap with several other disorders, including Saethre-Chotzen syndrome. {ECO:0000269|PubMed:15964893}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: DNA-dependent ATPase. May modulate chromosome segregation. {ECO:0000269|PubMed:15317757}.; ","gedi|level2",{"$nulls":3},"p.Leu913Phe","c.2739G>C","MODERATE","913/1208",15,{"$nulls":5},"5","476","875","371","668","368","684","0","0","0","0.098",{"$nulls":20},"2.798489",null,".;3.2",null,null,".;0.996",null,"0.499;0.526",{"$nulls":3},"Unknown",-1,"AR","Baller-Gerold syndrome; RAPADILINO syndrome; Rothmund-Thomson syndrome","Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dermatologic; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Oncologic; Renal","COSMIC,vCIN",null,null,"C0265308| C1849453| C5203410","0/0","448,0","0","448","0/1","769,68","0.0812","837",null,"chr8:144512863:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0823"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RELA","chr11:65662086","RELA(P13A)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving C11orf95 is found in more than two-thirds of supratentorial ependymomas. Translocation with C11orf95 produces a C11orf95-RELA fusion protein. C11orf95-RELA translocations are potent oncogenes that probably transform neural stem cells by driving an aberrant NF- kappa-B transcription program (PubMed:24553141). {ECO:0000269|PubMed:24553141}.; ","FUNCTION: NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52. The heterodimeric RELA- NFKB1 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. The NF-kappa-B heterodimeric RELA-NFKB1 and RELA-REL complexes, for instance, function as transcriptional activators. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF- kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. The inhibitory effect of I-kappa-B on NF-kappa-B through retention in the cytoplasm is exerted primarily through the interaction with RELA. RELA shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Beside its activity as a direct transcriptional activator, it is also able to modulate promoters accessibility to transcription factors and thereby indirectly regulate gene expression. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1. Essential for cytokine gene expression in T-cells (PubMed:15790681). The NF-kappa-B homodimeric RELA-RELA complex appears to be involved in invasin- mediated activation of IL-8 expression. {ECO:0000269|PubMed:10928981, ECO:0000269|PubMed:12748188, ECO:0000269|PubMed:15790681, ECO:0000269|PubMed:17000776, ECO:0000269|PubMed:17620405, ECO:0000269|PubMed:19058135, ECO:0000269|PubMed:19103749, ECO:0000269|PubMed:20547752}.; ","level2",{"$nulls":3},"p.Pro13Ala","c.37C>G","MODERATE","13/551",3,{"$nulls":5},"5","265","281","182","195","249","263","0","0","0","0.1217",{"$nulls":20},"2.999155","0.68;.;.;0.75;0.68;0.82;.;.","1.095;.;.;.;1.095;.;.;.","0.994232","-1.48;.;.;-1.46;-1.48;-1.49;-1.64;-1.47","0.634;.;.;0.002;0.75;.;.;.","0.004;.;.;0.04;0.004;0.014;0.054;0.05","0.272;0.245;0.29;0.245;0.245;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS,kCANCER,kMAPK",null,null,"C4748997","0/0","264,0","0","264","0/1","247,34","0.121","281",null,"chr11:65662086:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1231"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RELA","chr11:65662086","RELA(P13A)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving C11orf95 is found in more than two-thirds of supratentorial ependymomas. Translocation with C11orf95 produces a C11orf95-RELA fusion protein. C11orf95-RELA translocations are potent oncogenes that probably transform neural stem cells by driving an aberrant NF- kappa-B transcription program (PubMed:24553141). {ECO:0000269|PubMed:24553141}.; ","FUNCTION: NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52. The heterodimeric RELA- NFKB1 complex appears to be most abundant one. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. The NF-kappa-B heterodimeric RELA-NFKB1 and RELA-REL complexes, for instance, function as transcriptional activators. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF- kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. The inhibitory effect of I-kappa-B on NF-kappa-B through retention in the cytoplasm is exerted primarily through the interaction with RELA. RELA shows a weak DNA-binding site which could contribute directly to DNA binding in the NF-kappa-B complex. Beside its activity as a direct transcriptional activator, it is also able to modulate promoters accessibility to transcription factors and thereby indirectly regulate gene expression. Associates with chromatin at the NF-kappa-B promoter region via association with DDX1. Essential for cytokine gene expression in T-cells (PubMed:15790681). The NF-kappa-B homodimeric RELA-RELA complex appears to be involved in invasin- mediated activation of IL-8 expression. {ECO:0000269|PubMed:10928981, ECO:0000269|PubMed:12748188, ECO:0000269|PubMed:15790681, ECO:0000269|PubMed:17000776, ECO:0000269|PubMed:17620405, ECO:0000269|PubMed:19058135, ECO:0000269|PubMed:19103749, ECO:0000269|PubMed:20547752}.; ","level2",{"$nulls":3},"p.Pro13Ala","c.37C>G","MODERATE","13/551",3,{"$nulls":5},"5","265","329","182","224","250","295","0","0","0","0.0915",{"$nulls":20},"2.999155","0.68;.;.;0.75;0.68;0.82;.;.","1.095;.;.;.;1.095;.;.;.","0.994232","-1.48;.;.;-1.46;-1.48;-1.49;-1.64;-1.47","0.634;.;.;0.002;0.75;.;.;.","0.004;.;.;0.04;0.004;0.014;0.054;0.05","0.272;0.245;0.29;0.245;0.245;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS,kCANCER,kMAPK",null,null,"C4748997","0/0","264,0","0","264","0/1","295,28","0.0867","323",null,"chr11:65662086:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0759"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RFX1","chr19:13973110","RFX1(S316C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.; ",{"$nulls":4},"p.Ser316Cys","c.947C>G","MODERATE","316/979",9,{"$nulls":5},"5","278","289","190","203","253","260","0","0","0","0.0731",{"$nulls":20},"3.566455","0.75","1.7","0.999076","-1.98","0.974","0.01","0.199",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","259,0","0","259","0/1","249,21","0.0778","270",null,"chr19:13973110:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0788"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RFX1","chr19:13973110","RFX1(S316C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.; ",{"$nulls":4},"p.Ser316Cys","c.947C>G","MODERATE","316/979",9,{"$nulls":5},"5","278","389","190","260","250","353","0","0","0","0.0737",{"$nulls":20},"3.566455","0.75","1.7","0.999076","-1.98","0.974","0.01","0.199",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","261,0","0","261","0/1","335,24","0.0669","359",null,"chr19:13973110:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0615"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RHOBTB1","chr10:60888510","RHOBTB1(Q386H)",null,null,"domain (BTB 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln386His","c.1158A>T","MODERATE","386/696",6,{"$nulls":5},"4","938","1102","728","828","790","914","0","0","0","0.3096",{"$nulls":20},"2.527434","2.43","0.69","0.595007","-1.02","0.586","0.168","0.402;0.387",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","899,0","0","899","0/1","716,320","0.3089","1036",null,"chr10:60888510:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2911"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RHOBTB1","chr10:60888510","RHOBTB1(Q386H)",null,null,"domain (BTB 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln386His","c.1158A>T","MODERATE","386/696",6,{"$nulls":5},"4","938","1210","728","900","790","1057","0","0","0","0.1315",{"$nulls":20},"2.527434","2.43","0.69","0.595007","-1.02","0.586","0.168","0.402;0.387",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","903,0","0","903","0/1","1017,148","0.127","1165",null,"chr10:60888510:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1256"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RIMBP2","chr12:130442022","RIMBP2(E427K)",null,null,"domain (Fibronectin type-III 2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1209743356",-1,null,"FUNCTION: Plays a role in the synaptic transmission as bifunctional linker that interacts simultaneously with RIMS1, RIMS2, CACNA1D and CACNA1B. {ECO:0000250}.; ",{"$nulls":4},"p.Glu427Lys","c.1279G>A","MODERATE","427/1052",8,{"$nulls":5},"4","918","880","678","670","811","739","0","0","0","0.2043",{"$nulls":20},"2.818581","0.57;.;.","1.955;.;.","0.964889","-2.54;.;.","0.91;.;.","0.456;.;.","0.534;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","900,0","0","900","0/1","692,165","0.1925","857",null,"chr12:130442022:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1896"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RIMBP2","chr12:130442022","RIMBP2(E427K)",null,null,"domain (Fibronectin type-III 2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1209743356",-1,null,"FUNCTION: Plays a role in the synaptic transmission as bifunctional linker that interacts simultaneously with RIMS1, RIMS2, CACNA1D and CACNA1B. {ECO:0000250}.; ",{"$nulls":4},"p.Glu427Lys","c.1279G>A","MODERATE","427/1052",8,{"$nulls":5},"4","918","991","678","742","813","832","0","0","0","0.0805",{"$nulls":20},"2.818581","0.57;.;.","1.955;.;.","0.964889","-2.54;.;.","0.91;.;.","0.456;.;.","0.534;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","906,0","0","906","0/1","896,71","0.0734","967",null,"chr12:130442022:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0768"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RING1","chr6:33212334","RING1(E386K)",null,null,"region of interest (Necessary for interaction with CBX2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Constitutes one of the E3 ubiquitin-protein ligases that mediate monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. Compared to RNF2/RING2, it does not have the main E3 ubiquitin ligase activity on histone H2A, and it may rather act as a modulator of RNF2/RING2 activity. {ECO:0000269|PubMed:16359901}.; ",{"$nulls":4},"p.Glu386Lys","c.1156G>A","MODERATE","386/406",7,{"$nulls":5},"4","405","456","285","317","349","377","0","0","0","0.1857",{"$nulls":20},"4.415266","-2.35","2.095","0.999975","-3.13","0.993","0.004","0.587",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","385,0","0","385","0/1","346,80","0.1878","426",null,"chr6:33212334:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1767"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RING1","chr6:33212334","RING1(E386K)",null,null,"region of interest (Necessary for interaction with CBX2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Constitutes one of the E3 ubiquitin-protein ligases that mediate monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. Compared to RNF2/RING2, it does not have the main E3 ubiquitin ligase activity on histone H2A, and it may rather act as a modulator of RNF2/RING2 activity. {ECO:0000269|PubMed:16359901}.; ",{"$nulls":4},"p.Glu386Lys","c.1156G>A","MODERATE","386/406",7,{"$nulls":5},"4","405","440","285","298","345","374","0","0","0","0.0749",{"$nulls":20},"4.415266","-2.35","2.095","0.999975","-3.13","0.993","0.004","0.587",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","378,0","0","378","0/1","369,28","0.0705","397",null,"chr6:33212334:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0705"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RIPK1","chr6:3104307","RIPK1(S333*)",null,null,"region of interest (Interaction with SQSTM1 ), modified residue (Phosphoserine; by MAP3K7)",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Serine-threonine kinase which transduces inflammatory and cell-death signals (programmed necrosis) following death receptors ligation, activation of pathogen recognition receptors (PRRs), and DNA damage (PubMed:11101870, PubMed:17389591, PubMed:19524512, PubMed:19524513). Upon activation of TNFR1 by the TNF-alpha family cytokines, TRADD and TRAF2 are recruited to the receptor (PubMed:11101870, PubMed:17389591, PubMed:19524512, PubMed:19524513). Phosphorylates DAB2IP at 'Ser-728' in a TNF- alpha-dependent manner, and thereby activates the MAP3K5-JNK apoptotic cascade (PubMed:17389591). Ubiquitination by TRAF2 via 'Lys-63'-link chains acts as a critical enhancer of communication with downstream signal transducers in the mitogen-activated protein kinase pathway and the NF-kappa-B pathway, which in turn mediate downstream events including the activation of genes encoding inflammatory molecules (PubMed:15258597). Polyubiquitinated protein binds to IKBKG/NEMO, the regulatory subunit of the IKK complex, a critical event for NF-kappa-B activation. Interaction with other cellular RHIM-containing adapters initiates gene activation and cell death (PubMed:15258597). RIPK1 and RIPK3 association, in particular, forms a necrosis-inducing complex (PubMed:19524513, PubMed:19524512). {ECO:0000269|PubMed:11101870, ECO:0000269|PubMed:15258597, ECO:0000269|PubMed:17389591, ECO:0000269|PubMed:19524512, ECO:0000269|PubMed:19524513}.; ","level2",{"$nulls":3},"p.Ser333*","c.998C>G","HIGH","333/671",8,{"$nulls":5},"5","234","248","141","167","223","226","0","0","0","0.0929",{"$nulls":5},"(RIPK1|ENSG00000137275|1|1.00)","(RIPK1|ENSG00000137275|1|1.00)",{"$nulls":13},"7.624514",null,null,"1",{"$nulls":3},"0.938",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS",null,null,"C4748212| CN280858","0/0","229,0","0","229","0/1","219,23","0.095","242",null,"chr6:3104307:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0838"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RIPK1","chr6:3104307","RIPK1(S333*)",null,null,"region of interest (Interaction with SQSTM1 ), modified residue (Phosphoserine; by MAP3K7)",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Serine-threonine kinase which transduces inflammatory and cell-death signals (programmed necrosis) following death receptors ligation, activation of pathogen recognition receptors (PRRs), and DNA damage (PubMed:11101870, PubMed:17389591, PubMed:19524512, PubMed:19524513). Upon activation of TNFR1 by the TNF-alpha family cytokines, TRADD and TRAF2 are recruited to the receptor (PubMed:11101870, PubMed:17389591, PubMed:19524512, PubMed:19524513). Phosphorylates DAB2IP at 'Ser-728' in a TNF- alpha-dependent manner, and thereby activates the MAP3K5-JNK apoptotic cascade (PubMed:17389591). Ubiquitination by TRAF2 via 'Lys-63'-link chains acts as a critical enhancer of communication with downstream signal transducers in the mitogen-activated protein kinase pathway and the NF-kappa-B pathway, which in turn mediate downstream events including the activation of genes encoding inflammatory molecules (PubMed:15258597). Polyubiquitinated protein binds to IKBKG/NEMO, the regulatory subunit of the IKK complex, a critical event for NF-kappa-B activation. Interaction with other cellular RHIM-containing adapters initiates gene activation and cell death (PubMed:15258597). RIPK1 and RIPK3 association, in particular, forms a necrosis-inducing complex (PubMed:19524513, PubMed:19524512). {ECO:0000269|PubMed:11101870, ECO:0000269|PubMed:15258597, ECO:0000269|PubMed:17389591, ECO:0000269|PubMed:19524512, ECO:0000269|PubMed:19524513}.; ","level2",{"$nulls":3},"p.Ser333*","c.998C>G","HIGH","333/671",8,{"$nulls":5},"5","234","252","141","176","221","227","0","0","0","0.0617",{"$nulls":5},"(RIPK1|ENSG00000137275|1|1.00)","(RIPK1|ENSG00000137275|1|1.00)",{"$nulls":13},"7.624514",null,null,"1",{"$nulls":3},"0.938",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS",null,null,"C4748212| CN280858","0/0","229,0","0","229","0/1","224,21","0.0857","245",null,"chr6:3104307:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0909"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RMDN2","chr2:37951910","RMDN2(A232G)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala232Gly","c.695C>G","MODERATE","232/573",2,{"$nulls":5},"5","469","562","359","409","423","489","0","0","0","0.1309",{"$nulls":20},"0.100492","0.79;0.79;.",null,"1","-1.46;-1.46;-1.71",null,"0.28;0.28;0.359","0.113;0.119;0.089",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","452,0","0","452","0/1","468,71","0.1317","539",null,"chr2:37951910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1345"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RMDN2","chr2:37951910","RMDN2(A232G)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala232Gly","c.695C>G","MODERATE","232/573",2,{"$nulls":5},"4","469","555","359","412",null,null,"0","0",{"$nulls":22},"0.100492","0.79;0.79;.",null,"1","-1.46;-1.46;-1.71",null,"0.28;0.28;0.359","0.113;0.119;0.089",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","457,0","0","457","0/1","499,30","0.0567","529",null,"chr2:37951910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0607"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RNF148","chr7:122702125","RNF148(C209Y)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Cys209Tyr","c.626G>A","MODERATE","209/305",1,{"$nulls":5},"4","637","728","510","589","571","628","0","0","0","0.1306",{"$nulls":20},"0.987066","3.59","1.67","1;1;1;1;0.991433;1","0.89",null,"0.209","0.345",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","616,1","0.0016","617","0/1","614,96","0.1352","710",null,"chr7:122702125:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1392"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RNF148","chr7:122702125","RNF148(C209Y)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Cys209Tyr","c.626G>A","MODERATE","209/305",1,{"$nulls":5},"5","637","742","510","583","572","654","0","0","0","0.0642",{"$nulls":20},"0.987066","3.59","1.67","1;1;1;1;0.991433;1","0.89",null,"0.209","0.345",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","619,0","0","619","0/1","688,45","0.0614","733",null,"chr7:122702125:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0669"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RNF19A","chr8:100259245","RNF19A(E610Q)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as SNCAIP or CASR. Specifically ubiquitinates pathogenic SOD1 variants, which leads to their proteasomal degradation and to neuronal protection. {ECO:0000269|PubMed:11237715, ECO:0000269|PubMed:12145308, ECO:0000269|PubMed:12750386, ECO:0000269|PubMed:15456787, ECO:0000269|PubMed:16513638}.; ",{"$nulls":4},"p.Glu610Gln","c.1828G>C","MODERATE","610/838",10,{"$nulls":5},"5","151","333","123","268","139","304","0","0","0","0.3947",{"$nulls":20},"3.76804","-1.81","0.69","0.999997","-1.11","0.201","0.006","0.261;0.259",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","150,0","0","150","0/1","196,138","0.4132","334",null,"chr8:100259245:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.4291"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RNF40","chr16:30768488","RNF40(R646Q)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs751895980",6.344e-05,null,"FUNCTION: Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes. {ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:19410543}.; ",{"$nulls":4},"p.Arg646Gln","c.1937G>A","MODERATE","646/1001",13,{"$nulls":5},"4","520","561","424","441","421","460","0.0019","0.0019","0","0.25",{"$nulls":20},"3.242788","1.49;1.5;1.49","1.845;.;.","0.999983;0.999995;0.999897;0.999983","-1.27;-1.27;-1.2","0.995;.;0.999","0.096;0.056;0.114","0.36;0.366;0.344",{"$nulls":3},"ExAC_SAS_AF",6.344e-05,{"$nulls":7},"0/0","513,1","0.0019","514","0/1","416,134","0.2436","550",null,"chr16:30768488:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.254"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RNF40","chr16:30768488","RNF40(R646Q)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs751895980",6.344e-05,null,"FUNCTION: Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes. {ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:19410543}.; ",{"$nulls":4},"p.Arg646Gln","c.1937G>A","MODERATE","646/1001",13,{"$nulls":5},"4","520","623","424","489","421","503","0.0019","0.0019","0","0.163",{"$nulls":20},"3.242788","1.49;1.5;1.49","1.845;.;.","0.999983;0.999995;0.999897;0.999983","-1.27;-1.27;-1.2","0.995;.;0.999","0.096;0.056;0.114","0.36;0.366;0.344",{"$nulls":3},"ExAC_SAS_AF",6.344e-05,{"$nulls":7},"0/0","511,1","0.002","512","0/1","510,92","0.1528","602",null,"chr16:30768488:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1431"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RORB","chr9:74671852","RORB(L403H)",null,null,"domain (NR LBD ), sequence variant (In EIG15; loss of subcellular location in the nucleoplasm. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Nuclear receptor that binds DNA as a monomer to ROR response elements (RORE) containing a single core motif half-site 5'-AGGTCA-3' preceded by a short A-T-rich sequence. Considered to have intrinsic transcriptional activity, have some natural ligands such as all-trans retinoic acid (ATRA) and other retinoids which act as inverse agonists repressing the transcriptional activity. Required for normal postnatal development of rod and cone photoreceptor cells. Modulates rod photoreceptors differentiation at least by inducing the transcription factor NRL-mediated pathway. In cone photoreceptor cells, regulates transcription of OPN1SW. Involved in the regulation of the period length and stability of the circadian rhythm. May control cytoarchitectural patterning of neocortical neurons during development. May act in a dose-dependent manner to regulate barrel formation upon innervation of layer IV neurons by thalamocortical axons. May play a role in the suppression of osteoblastic differentiation through the inhibition of RUNX2 transcriptional activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu403His","c.1208T>A","MODERATE","403/470",9,{"$nulls":5},"5","199","199","146","139","175","164","0","0","0","0.2927",{"$nulls":20},"4.2538540000000005","-5.54",".;3.76","1","-5.81",".;1.0","0.0","0.923;0.92",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It is a DNA-binding protein that can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, and to help regulate the expression of some genes involved in circadian rhythm. [provided by RefSeq, Feb 2014].  ",null,"C5193050","0/0","187,0","0","187","0/1","134,59","0.3057","193",null,"chr9:74671852:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3022"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RORB","chr9:74671852","RORB(L403H)",null,null,"domain (NR LBD ), sequence variant (In EIG15; loss of subcellular location in the nucleoplasm. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Nuclear receptor that binds DNA as a monomer to ROR response elements (RORE) containing a single core motif half-site 5'-AGGTCA-3' preceded by a short A-T-rich sequence. Considered to have intrinsic transcriptional activity, have some natural ligands such as all-trans retinoic acid (ATRA) and other retinoids which act as inverse agonists repressing the transcriptional activity. Required for normal postnatal development of rod and cone photoreceptor cells. Modulates rod photoreceptors differentiation at least by inducing the transcription factor NRL-mediated pathway. In cone photoreceptor cells, regulates transcription of OPN1SW. Involved in the regulation of the period length and stability of the circadian rhythm. May control cytoarchitectural patterning of neocortical neurons during development. May act in a dose-dependent manner to regulate barrel formation upon innervation of layer IV neurons by thalamocortical axons. May play a role in the suppression of osteoblastic differentiation through the inhibition of RUNX2 transcriptional activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu403His","c.1208T>A","MODERATE","403/470",9,{"$nulls":5},"5","199","250","146","154","175","225","0","0","0","0.0933",{"$nulls":20},"4.2538540000000005","-5.54",".;3.76","1","-5.81",".;1.0","0.0","0.923;0.92",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the NR1 subfamily of nuclear hormone receptors. It is a DNA-binding protein that can bind as a monomer or as a homodimer to hormone response elements upstream of several genes to enhance the expression of those genes. The encoded protein has been shown to interact with NM23-2, a nucleoside diphosphate kinase involved in organogenesis and differentiation, and to help regulate the expression of some genes involved in circadian rhythm. [provided by RefSeq, Feb 2014].  ",null,"C5193050","0/0","190,0","0","190","0/1","220,22","0.0909","242",null,"chr9:74671852:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1039"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RP1L1","chr8:10610127","RP1L1(E1324fs)",{"$nulls":6},215,"PASS","Loss Of Function",null,-1,"DISEASE: Occult macular dystrophy (OCMD) [MIM:613587]: An inherited macular dystrophy characterized by progressive loss of macular function but normal ophthalmoscopic appearance. It is typically characterized by a central cone dysfunction leading to a loss of vision despite normal ophthalmoscopic appearance, normal fluorescein angiography, and normal full-field electroretinogram (ERGs), but the amplitudes of the focal macular ERGs and multifocal ERGs are significantly reduced at the central retina. {ECO:0000269|PubMed:20826268, ECO:0000269|PubMed:22605915}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for the differentiation of photoreceptor cells. Plays a role in the organization of outer segment of rod and cone photoreceptors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu1324fs","c.3970_3971insGGACTAAAGTAATAGG","HIGH","1324/2400",4,{"$nulls":5},"1",{"$nulls":15},"(RP1L1|ENSG00000183638|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Occult macular dystrophy; Retinitis pigmentosa, autosomal recessive","Ophthalmologic",{"$nulls":3},"C3150833| CN263396","0/0","380,0","0","461","0/1","255,61","0.1728","353",null,"chr8:10610127:T:TCCTATTACTTTAGTCC",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1728"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","RYR1","chr19:38585079","RYR1(L4929fs)",null,null,"transmembrane region (Helical; Name=6 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Malignant hyperthermia 1 (MHS1) [MIM:145600]: Autosomal dominant pharmacogenetic disorder of skeletal muscle and is one of the main causes of death due to anesthesia. In susceptible people, an MH episode can be triggered by all commonly used inhalational anesthetics such as halothane and by depolarizing muscle relaxants such as succinylcholine. The clinical features of the myopathy are hyperthermia, accelerated muscle metabolism, contractures, metabolic acidosis, tachycardia and death, if not treated with the postsynaptic muscle relaxant, dantrolene. Susceptibility to MH can be determined with the 'in vitro' contracture test (IVCT): observing the magnitude of contractures induced in strips of muscle tissue by caffeine alone and halothane alone. Patients with normal response are MH normal (MHN), those with abnormal response to caffeine alone or halothane alone are MH equivocal (MHE(C) and MHE(H) respectively). {ECO:0000269|PubMed:10051009, ECO:0000269|PubMed:10484775, ECO:0000269|PubMed:10612851, ECO:0000269|PubMed:10823104, ECO:0000269|PubMed:10888602, ECO:0000269|PubMed:11241852, ECO:0000269|PubMed:11389482, ECO:0000269|PubMed:11525881, ECO:0000269|PubMed:11575529, ECO:0000269|PubMed:11928716, ECO:0000269|PubMed:12059893, ECO:0000269|PubMed:12066726, ECO:0000269|PubMed:12123492, ECO:0000269|PubMed:12208234, ECO:0000269|PubMed:12411788, ECO:0000269|PubMed:12709367, ECO:0000269|PubMed:12883402, ECO:0000269|PubMed:1354642, ECO:0000269|PubMed:14732627, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:15221887, ECO:0000269|PubMed:15448513, ECO:0000269|PubMed:16163667, ECO:0000269|PubMed:1774074, ECO:0000269|PubMed:19191329, ECO:0000269|PubMed:19685112, ECO:0000269|PubMed:20142353, ECO:0000269|PubMed:20681998, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24013571, ECO:0000269|PubMed:26115329, ECO:0000269|PubMed:26381711, ECO:0000269|PubMed:26631338, ECO:0000269|PubMed:27586648, ECO:0000269|PubMed:7751854, ECO:0000269|PubMed:7849712, ECO:0000269|PubMed:7881417, ECO:0000269|PubMed:8012359, ECO:0000269|PubMed:8220423, ECO:0000269|PubMed:9066328, ECO:0000269|PubMed:9138151, ECO:0000269|PubMed:9389851, ECO:0000269|PubMed:9450902, ECO:0000269|PubMed:9497245}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Central core disease of muscle (CCD) [MIM:117000]: Autosomal dominant congenital myopathy, but a severe autosomal recessive form also exists. Both clinical and histological variability is observed. Affected individuals typically display hypotonia and proximal muscle weakness in infancy, leading to the delay of motor milestones. The clinical course of the disorder is usually slow or nonprogressive in adulthood, and the severity of the symptoms may vary from normal to significant muscle weakness. Microscopic examination of CCD-affected skeletal muscle reveals a predominance of type I fibers containing amorphous-looking areas (cores) that do not stain with oxidative and phosphorylase histochemical techniques. {ECO:0000269|PubMed:10097181, ECO:0000269|PubMed:11113224, ECO:0000269|PubMed:11709545, ECO:0000269|PubMed:11741831, ECO:0000269|PubMed:12112081, ECO:0000269|PubMed:12136074, ECO:0000269|PubMed:12565913, ECO:0000269|PubMed:12566385, ECO:0000269|PubMed:12937085, ECO:0000269|PubMed:14670767, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:17204054, ECO:0000269|PubMed:17226826, ECO:0000269|PubMed:18253926, ECO:0000269|PubMed:18312400, ECO:0000269|PubMed:20142353, ECO:0000269|PubMed:21674524, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24561095, ECO:0000269|PubMed:26381711, ECO:0000269|PubMed:27234031, ECO:0000269|PubMed:27586648, ECO:0000269|PubMed:7829078, ECO:0000269|PubMed:8220422, ECO:0000269|PubMed:8220423, ECO:0000269|PubMed:9497245}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiminicore disease with external ophthalmoplegia (MMDO) [MIM:255320]: Clinically heterogeneous neuromuscular disorder. General features include neonatal hypotonia, delayed motor development, and generalized muscle weakness and amyotrophy, which may progress slowly or remain stable. Muscle biopsy shows multiple, poorly circumscribed, short areas of sarcomere disorganization and mitochondria depletion (areas termed minicores) in most muscle fibers. Typically, no dystrophic signs, such as muscle fiber necrosis or regeneration or significant endomysial fibrosis, are present in multiminicore disease. {ECO:0000269|PubMed:12719381, ECO:0000269|PubMed:16380615, ECO:0000269|PubMed:20583297}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in RYR1 may be a cause of Samaritan myopathy, a congenital myopathy with benign course. Patients display severe hypotonia and respiratory distress at birth. Unlike other congenital myopathies, the health status constantly improves and patients are minimally affected at adulthood.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules (PubMed:11741831, PubMed:16163667). Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm (PubMed:18268335). Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity). {ECO:0000250|UniProtKB:E9PZQ0, ECO:0000269|PubMed:18268335, ECO:0000305|PubMed:11741831, ECO:0000305|PubMed:16163667}.; ","acmg",{"$nulls":3},"p.Leu4929fs","c.14785delC","HIGH","4929/5038",102,{"$nulls":5},"5","549","541","370","357","421","414","0","0","0","0.2343",{"$nulls":31},"Unknown",-1,"AD/AR","Malignant hyperthermia, susceptibility 1; Central core disease; Minicore myopathy; Multicore myopathy; Minicore myopathy with external ophthalmoplegia; Centronuclear myopathy (individuals with these conditions may also be at risk of malignant hyperthermia)","Cardiovascular; Musculoskeletal; Renal",{"$nulls":3},"CN181199| C0751951| C1850674| C2930980| C0546264","0/0","495,0","0","495","0/1","372,131","0.2604","503",null,"chr19:38585079:TC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2689"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","RYR1","chr19:38585079","RYR1(L4929fs)",null,null,"transmembrane region (Helical; Name=6 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Malignant hyperthermia 1 (MHS1) [MIM:145600]: Autosomal dominant pharmacogenetic disorder of skeletal muscle and is one of the main causes of death due to anesthesia. In susceptible people, an MH episode can be triggered by all commonly used inhalational anesthetics such as halothane and by depolarizing muscle relaxants such as succinylcholine. The clinical features of the myopathy are hyperthermia, accelerated muscle metabolism, contractures, metabolic acidosis, tachycardia and death, if not treated with the postsynaptic muscle relaxant, dantrolene. Susceptibility to MH can be determined with the 'in vitro' contracture test (IVCT): observing the magnitude of contractures induced in strips of muscle tissue by caffeine alone and halothane alone. Patients with normal response are MH normal (MHN), those with abnormal response to caffeine alone or halothane alone are MH equivocal (MHE(C) and MHE(H) respectively). {ECO:0000269|PubMed:10051009, ECO:0000269|PubMed:10484775, ECO:0000269|PubMed:10612851, ECO:0000269|PubMed:10823104, ECO:0000269|PubMed:10888602, ECO:0000269|PubMed:11241852, ECO:0000269|PubMed:11389482, ECO:0000269|PubMed:11525881, ECO:0000269|PubMed:11575529, ECO:0000269|PubMed:11928716, ECO:0000269|PubMed:12059893, ECO:0000269|PubMed:12066726, ECO:0000269|PubMed:12123492, ECO:0000269|PubMed:12208234, ECO:0000269|PubMed:12411788, ECO:0000269|PubMed:12709367, ECO:0000269|PubMed:12883402, ECO:0000269|PubMed:1354642, ECO:0000269|PubMed:14732627, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:15221887, ECO:0000269|PubMed:15448513, ECO:0000269|PubMed:16163667, ECO:0000269|PubMed:1774074, ECO:0000269|PubMed:19191329, ECO:0000269|PubMed:19685112, ECO:0000269|PubMed:20142353, ECO:0000269|PubMed:20681998, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24013571, ECO:0000269|PubMed:26115329, ECO:0000269|PubMed:26381711, ECO:0000269|PubMed:26631338, ECO:0000269|PubMed:27586648, ECO:0000269|PubMed:7751854, ECO:0000269|PubMed:7849712, ECO:0000269|PubMed:7881417, ECO:0000269|PubMed:8012359, ECO:0000269|PubMed:8220423, ECO:0000269|PubMed:9066328, ECO:0000269|PubMed:9138151, ECO:0000269|PubMed:9389851, ECO:0000269|PubMed:9450902, ECO:0000269|PubMed:9497245}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Central core disease of muscle (CCD) [MIM:117000]: Autosomal dominant congenital myopathy, but a severe autosomal recessive form also exists. Both clinical and histological variability is observed. Affected individuals typically display hypotonia and proximal muscle weakness in infancy, leading to the delay of motor milestones. The clinical course of the disorder is usually slow or nonprogressive in adulthood, and the severity of the symptoms may vary from normal to significant muscle weakness. Microscopic examination of CCD-affected skeletal muscle reveals a predominance of type I fibers containing amorphous-looking areas (cores) that do not stain with oxidative and phosphorylase histochemical techniques. {ECO:0000269|PubMed:10097181, ECO:0000269|PubMed:11113224, ECO:0000269|PubMed:11709545, ECO:0000269|PubMed:11741831, ECO:0000269|PubMed:12112081, ECO:0000269|PubMed:12136074, ECO:0000269|PubMed:12565913, ECO:0000269|PubMed:12566385, ECO:0000269|PubMed:12937085, ECO:0000269|PubMed:14670767, ECO:0000269|PubMed:14985404, ECO:0000269|PubMed:17204054, ECO:0000269|PubMed:17226826, ECO:0000269|PubMed:18253926, ECO:0000269|PubMed:18312400, ECO:0000269|PubMed:20142353, ECO:0000269|PubMed:21674524, ECO:0000269|PubMed:23558838, ECO:0000269|PubMed:24561095, ECO:0000269|PubMed:26381711, ECO:0000269|PubMed:27234031, ECO:0000269|PubMed:27586648, ECO:0000269|PubMed:7829078, ECO:0000269|PubMed:8220422, ECO:0000269|PubMed:8220423, ECO:0000269|PubMed:9497245}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiminicore disease with external ophthalmoplegia (MMDO) [MIM:255320]: Clinically heterogeneous neuromuscular disorder. General features include neonatal hypotonia, delayed motor development, and generalized muscle weakness and amyotrophy, which may progress slowly or remain stable. Muscle biopsy shows multiple, poorly circumscribed, short areas of sarcomere disorganization and mitochondria depletion (areas termed minicores) in most muscle fibers. Typically, no dystrophic signs, such as muscle fiber necrosis or regeneration or significant endomysial fibrosis, are present in multiminicore disease. {ECO:0000269|PubMed:12719381, ECO:0000269|PubMed:16380615, ECO:0000269|PubMed:20583297}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in RYR1 may be a cause of Samaritan myopathy, a congenital myopathy with benign course. Patients display severe hypotonia and respiratory distress at birth. Unlike other congenital myopathies, the health status constantly improves and patients are minimally affected at adulthood.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules (PubMed:11741831, PubMed:16163667). Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm (PubMed:18268335). Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity). {ECO:0000250|UniProtKB:E9PZQ0, ECO:0000269|PubMed:18268335, ECO:0000305|PubMed:11741831, ECO:0000305|PubMed:16163667}.; ","acmg",{"$nulls":3},"p.Leu4929fs","c.14785delC","HIGH","4929/5038",102,{"$nulls":5},"5","549","616","370","409","421","459","0","0","0","0.1264",{"$nulls":31},"Unknown",-1,"AD/AR","Malignant hyperthermia, susceptibility 1; Central core disease; Minicore myopathy; Multicore myopathy; Minicore myopathy with external ophthalmoplegia; Centronuclear myopathy (individuals with these conditions may also be at risk of malignant hyperthermia)","Cardiovascular; Musculoskeletal; Renal",{"$nulls":3},"CN181199| C0751951| C1850674| C2930980| C0546264","0/0","497,0","0","497","0/1","491,76","0.134","567",null,"chr19:38585079:TC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1271"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SCN1A","chr2:165992159","SCN1A(N1706H)",null,null,"topological domain (Extracellular ), repeat (IV ), sequence variant (In EIEE6. ), sequence variant (In EIEE6. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Generalized epilepsy with febrile seizures plus 2 (GEFS+2) [MIM:604403]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269|PubMed:10742094, ECO:0000269|PubMed:11254444, ECO:0000269|PubMed:11254445, ECO:0000269|PubMed:11524484, ECO:0000269|PubMed:11756608, ECO:0000269|PubMed:12535936, ECO:0000269|PubMed:12576172, ECO:0000269|PubMed:12919402, ECO:0000269|PubMed:14672992, ECO:0000269|PubMed:15525788, ECO:0000269|PubMed:15694566, ECO:0000269|PubMed:15715999, ECO:0000269|PubMed:16525050, ECO:0000269|PubMed:17347258, ECO:0000269|PubMed:17507202, ECO:0000269|PubMed:17561957, ECO:0000269|PubMed:17927801, ECO:0000269|PubMed:17928445, ECO:0000269|PubMed:18251839, ECO:0000269|PubMed:18413471, ECO:0000269|PubMed:18566737, ECO:0000269|PubMed:19339291, ECO:0000269|PubMed:19464195, ECO:0000269|PubMed:19522081, ECO:0000269|PubMed:20117752, ECO:0000269|PubMed:20550552, ECO:0000269|PubMed:20600615, ECO:0000269|PubMed:20729507, ECO:0000269|PubMed:21248271, ECO:0000269|PubMed:21864321}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 6 (EIEE6) [MIM:607208]: A severe form of epileptic encephalopathy characterized by generalized tonic, clonic, and tonic-clonic seizures that are initially induced by fever and begin during the first year of life. Later, patients also manifest other seizure types, including absence, myoclonic, and simple and complex partial seizures. Psychomotor development delay is observed around the second year of life. Some patients manifest a borderline disease phenotype and do not necessarily fulfill all diagnostic criteria for core EIEE6. EIEE6 is considered to be the most severe phenotype within the spectrum of generalized epilepsies with febrile seizures-plus. {ECO:0000269|PubMed:11359211, ECO:0000269|PubMed:12083760, ECO:0000269|PubMed:12566275, ECO:0000269|PubMed:12754708, ECO:0000269|PubMed:12821740, ECO:0000269|PubMed:14504318, ECO:0000269|PubMed:14672992, ECO:0000269|PubMed:14738421, ECO:0000269|PubMed:15087100, ECO:0000269|PubMed:15944908, ECO:0000269|PubMed:16122630, ECO:0000269|PubMed:16458823, ECO:0000269|PubMed:16713920, ECO:0000269|PubMed:17054684, ECO:0000269|PubMed:17054685, ECO:0000269|PubMed:17129991, ECO:0000269|PubMed:17347258, ECO:0000269|PubMed:17561957, ECO:0000269|PubMed:18413471, ECO:0000269|PubMed:18639757, ECO:0000269|PubMed:18930999, ECO:0000269|PubMed:19522081, ECO:0000269|PubMed:19563458, ECO:0000269|PubMed:19589774, ECO:0000269|PubMed:19783390, ECO:0000269|PubMed:20110217, ECO:0000269|PubMed:20431604, ECO:0000269|PubMed:20452746, ECO:0000269|PubMed:20522430, ECO:0000269|PubMed:20729507, ECO:0000269|PubMed:21248271, ECO:0000269|PubMed:21864321, ECO:0000269|PubMed:22092154, ECO:0000269|PubMed:22612257, ECO:0000269|PubMed:23195492, ECO:0000269|PubMed:23662938, ECO:0000269|PubMed:23708187, ECO:0000269|PubMed:25818041, ECO:0000269|PubMed:26993267, ECO:0000269|PubMed:27864847, ECO:0000269|PubMed:28544625}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Intractable childhood epilepsy with generalized tonic- clonic seizures (ICEGTC) [MIM:607208]: A disorder characterized by generalized tonic-clonic seizures beginning usually in infancy and induced by fever. Seizures are associated with subsequent mental decline, as well as ataxia or hypotonia. ICEGTC is similar to SMEI, except for the absence of myoclonic seizures. {ECO:0000269|PubMed:12566275, ECO:0000269|PubMed:16210358, ECO:0000269|PubMed:17507202, ECO:0000269|PubMed:23195492, ECO:0000269|PubMed:23708187}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Migraine, familial hemiplegic, 3 (FHM3) [MIM:609634]: A subtype of migraine associated with transient blindness in some families. Migraine is a disabling symptom complex of periodic headaches, usually temporal and unilateral. Headaches are often accompanied by irritability, nausea, vomiting and photophobia, preceded by constriction of the cranial arteries. The two major subtypes are common migraine (migraine without aura) and classic migraine (migraine with aura). Classic migraine is characterized by recurrent attacks of reversible neurological symptoms (aura) that precede or accompany the headache. Aura may include a combination of sensory disturbances, such as blurred vision, hallucinations, vertigo, numbness and difficulty in concentrating and speaking. {ECO:0000269|PubMed:16054936, ECO:0000269|PubMed:17397047, ECO:0000269|PubMed:18021921, ECO:0000269|PubMed:19332696}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Febrile seizures, familial, 3A (FEB3A) [MIM:604403]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269|PubMed:16326807, ECO:0000269|PubMed:19522081}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=SCN1A mutations may be involved in Panayiotopoulos syndrome, a benign age-related focal seizure disorder occurring in early and mid-childhood. It is characterized by seizures, often prolonged, with predominantly autonomic symptoms, and by an electroencephalogram that shows shifting and/or multiple foci, often with occipital predominance. Autonomic seizures in Panayiotopoulos syndrome consist of episodes of disturbed autonomic function with emesis as the predominant symptom. Cardiorespiratory arrest is exceptional. {ECO:0000269|PubMed:17679682, ECO:0000269|PubMed:19339291, ECO:0000269|PubMed:19522081}.; ","FUNCTION: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in somatosensory neurons induces pain without neurogenic inflammation and produces hypersensitivity to mechanical, but not thermal stimuli. {ECO:0000250|UniProtKB:A2APX8}.; ","epilepsy",{"$nulls":3},"p.Asn1706His","c.5116A>C","MODERATE","1706/2009",28,{"$nulls":5},"4","647","918","540","745","554","468","0","0","0","0.1154",{"$nulls":20},"3.670664",".;.;.;-5.16;.;-5.16;.;-5.16;-5.16",".;.;.;2.66;.;2.66;.;.;.","0.999999",".;.;.;-4.36;.;-4.36;.;-4.36;-4.35",".;.;.;.;1.0;.;1.0;1.0;.",".;.;.;0.0;.;0.0;.;0.0;0.0",".;.;.;0.918;.;0.926;.;0.93;0.969",{"$nulls":3},"Unknown",-1,"AD","Migraine, familial hemiplegic 3","Neurologic",{"$nulls":3},"C1858673| C1864987| C4551549","0/0","642,0","0","642","0/1","810,94","0.104","904",null,"chr2:165992159:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1087"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SCNN1A","chr12:6362178","SCNN1A(E309K)",null,null,"topological domain (Extracellular ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Pseudohypoaldosteronism 1, autosomal recessive (PHA1B) [MIM:264350]: A rare salt wasting disease resulting from target organ unresponsiveness to mineralocorticoids. PHA1B is a severe form involving multiple organ systems, and characterized by an often fulminant presentation in the neonatal period with dehydration, hyponatremia, hyperkalemia, metabolic acidosis, failure to thrive and weight loss. {ECO:0000269|PubMed:10586178, ECO:0000269|PubMed:15853823, ECO:0000269|PubMed:18634878}. Note=The disease is caused by mutations affecting the gene represented in this entry. The degree of channel function impairment differentially affects the renin-aldosterone system and urinary Na/K ratios, resulting in distinct genotype-phenotype relationships in PHA1 patients. Loss-of-function mutations are associated with a severe clinical course and age-dependent hyperactivation of the renin-aldosterone system. This feature is not observed in patients with missense mutations that reduce but do not eliminate channel function. Markedly reduced channel activity results in impaired linear growth and delayed puberty (PubMed:18634878). {ECO:0000269|PubMed:18634878}.; DISEASE: Bronchiectasis with or without elevated sweat chloride 2 (BESC2) [MIM:613021]: A debilitating respiratory disease characterized by chronic, abnormal dilatation of the bronchi and other cystic fibrosis-like symptoms in the absence of known causes of bronchiectasis (cystic fibrosis, autoimmune diseases, ciliary dyskinesia, common variable immunodeficiency, foreign body obstruction). Clinical features include sub-normal lung function, sinopulmonary infections, chronic productive cough, excessive sputum production, and elevated sweat chloride in some cases. {ECO:0000269|PubMed:19462466}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sodium permeable non-voltage-sensitive ion channel inhibited by the diuretic amiloride. Mediates the electrodiffusion of the luminal sodium (and water, which follows osmotically) through the apical membrane of epithelial cells. Plays an essential role in electrolyte and blood pressure homeostasis, but also in airway surface liquid homeostasis, which is important for proper clearance of mucus. Controls the reabsorption of sodium in kidney, colon, lung and eccrine sweat glands. Also plays a role in taste perception. {ECO:0000269|PubMed:24124190, ECO:0000269|PubMed:8278374}.; ",{"$nulls":4},"p.Glu309Lys","c.925G>A","MODERATE","309/728",3,{"$nulls":5},"5","909","1096","623","752","809","951","0","0","0","0.0915",{"$nulls":20},"4.114144","-1.13;-1.07;-0.69;-1.11",".;3.115;.;.","0.999825;0.999825;0.999825;0.999825;0.999825;1","-3.79;-3.62;-3.65;-3.76","0.907;0.923;.;.","0.002;0.003;0.002;0.003","0.906;0.899;0.885;0.909",{"$nulls":3},"Unknown",-1,"AR/Digenic (with CFTR or other SCCN1 genes)","Pseudohypoaldosteronism, type I; Bronchiectasis with or without elevated sweat chloride 2","Allergy/Immunology/Infectious; Pulmonary; Renal",{"$nulls":3},"C1449843| C4748292| C2751666","0/0","874,0","0","874","0/1","922,100","0.0978","1022",null,"chr12:6362178:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0957"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SCNN1A","chr12:6362178","SCNN1A(E309K)",null,null,"topological domain (Extracellular ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Pseudohypoaldosteronism 1, autosomal recessive (PHA1B) [MIM:264350]: A rare salt wasting disease resulting from target organ unresponsiveness to mineralocorticoids. PHA1B is a severe form involving multiple organ systems, and characterized by an often fulminant presentation in the neonatal period with dehydration, hyponatremia, hyperkalemia, metabolic acidosis, failure to thrive and weight loss. {ECO:0000269|PubMed:10586178, ECO:0000269|PubMed:15853823, ECO:0000269|PubMed:18634878}. Note=The disease is caused by mutations affecting the gene represented in this entry. The degree of channel function impairment differentially affects the renin-aldosterone system and urinary Na/K ratios, resulting in distinct genotype-phenotype relationships in PHA1 patients. Loss-of-function mutations are associated with a severe clinical course and age-dependent hyperactivation of the renin-aldosterone system. This feature is not observed in patients with missense mutations that reduce but do not eliminate channel function. Markedly reduced channel activity results in impaired linear growth and delayed puberty (PubMed:18634878). {ECO:0000269|PubMed:18634878}.; DISEASE: Bronchiectasis with or without elevated sweat chloride 2 (BESC2) [MIM:613021]: A debilitating respiratory disease characterized by chronic, abnormal dilatation of the bronchi and other cystic fibrosis-like symptoms in the absence of known causes of bronchiectasis (cystic fibrosis, autoimmune diseases, ciliary dyskinesia, common variable immunodeficiency, foreign body obstruction). Clinical features include sub-normal lung function, sinopulmonary infections, chronic productive cough, excessive sputum production, and elevated sweat chloride in some cases. {ECO:0000269|PubMed:19462466}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sodium permeable non-voltage-sensitive ion channel inhibited by the diuretic amiloride. Mediates the electrodiffusion of the luminal sodium (and water, which follows osmotically) through the apical membrane of epithelial cells. Plays an essential role in electrolyte and blood pressure homeostasis, but also in airway surface liquid homeostasis, which is important for proper clearance of mucus. Controls the reabsorption of sodium in kidney, colon, lung and eccrine sweat glands. Also plays a role in taste perception. {ECO:0000269|PubMed:24124190, ECO:0000269|PubMed:8278374}.; ",{"$nulls":4},"p.Glu309Lys","c.925G>A","MODERATE","309/728",3,{"$nulls":5},"5","909","1231","623","838","808","1076","0","0","0","0.0576",{"$nulls":20},"4.114144","-1.13;-1.07;-0.69;-1.11",".;3.115;.;.","0.999825;0.999825;0.999825;0.999825;0.999825;1","-3.79;-3.62;-3.65;-3.76","0.907;0.923;.;.","0.002;0.003;0.002;0.003","0.906;0.899;0.885;0.909",{"$nulls":3},"Unknown",-1,"AR/Digenic (with CFTR or other SCCN1 genes)","Pseudohypoaldosteronism, type I; Bronchiectasis with or without elevated sweat chloride 2","Allergy/Immunology/Infectious; Pulmonary; Renal",{"$nulls":3},"C1449843| C4748292| C2751666","0/0","873,0","0","873","0/1","1078,72","0.0626","1150",null,"chr12:6362178:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0597"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SEMA6C","chr1:151132873","SEMA6C(A834P)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},39,"PASS","Missense",null,-1,null,"FUNCTION: Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections. {ECO:0000269|PubMed:12110693}.; ",{"$nulls":4},"p.Ala834Pro","c.2500G>C","MODERATE","834/962",20,{"$nulls":5},"1",{"$nulls":30},"0.023027","1.92;2.12;1.95;1.95",".;.;0.75;0.75","0.999917","-0.44;-0.44;-0.41;-0.41","0.003;0.0;0.002;0.002","0.086;0.09;0.089;0.089","0.078;0.069;0.086;0.084",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","45,0","0","45","0/1","44,3","0.0638","47",null,"chr1:151132873:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0638"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SERPING1","chr11:57600105","SERPING1(P128fs)",null,null,"disulfide bond , sequence variant (In HAE; phenotype consistent with hereditary angioedema type 2. )",{"$nulls":3},102,"PASS","Loss Of Function",null,-1,"DISEASE: Hereditary angioedema (HAE) [MIM:106100]: An autosomal dominant disorder characterized by episodic local swelling involving subcutaneous or submucous tissue of the upper respiratory and gastrointestinal tracts, face, extremities, and genitalia. Hereditary angioedema due to C1 esterase inhibitor deficiency is comprised of two clinically indistinguishable forms. In hereditary angioedema type 1, serum levels of C1 esterase inhibitor are decreased, while in type 2, the levels are normal or elevated, but the protein is non-functional. {ECO:0000269|PubMed:12773530, ECO:0000269|PubMed:1363816, ECO:0000269|PubMed:1451784, ECO:0000269|PubMed:14635117, ECO:0000269|PubMed:16409206, ECO:0000269|PubMed:2118657, ECO:0000269|PubMed:2296585, ECO:0000269|PubMed:22994404, ECO:0000269|PubMed:2365061, ECO:0000269|PubMed:24456027, ECO:0000269|PubMed:3178731, ECO:0000269|PubMed:7814636, ECO:0000269|PubMed:7883978, ECO:0000269|PubMed:8172583, ECO:0000269|PubMed:8529136, ECO:0000269|PubMed:8755917, ECO:0000269|Ref.41}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Activation of the C1 complex is under control of the C1- inhibitor. It forms a proteolytically inactive stoichiometric complex with the C1r or C1s proteases. May play a potentially crucial role in regulating important physiological pathways including complement activation, blood coagulation, fibrinolysis and the generation of kinins. Very efficient inhibitor of FXIIa. Inhibits chymotrypsin and kallikrein. {ECO:0000269|PubMed:8495195}.; ",{"$nulls":4},"p.Pro128fs","c.381dupG","HIGH","128/543",2,{"$nulls":5},"1",{"$nulls":15},"(SERPING1|ENSG00000149131|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Angioedema, hereditary","Allergy/Immunology/Infectious; Gastrointestinal",{"$nulls":3},"C2717906| C2717906| C1852700","0/0","194,0","0","194","0/1","157,11","0.0655","168",null,"chr11:57600105:A:AG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0655"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SFMBT2","chr10:7172068","SFMBT2(S748A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional repressor of HOXB13 gene. {ECO:0000269|PubMed:23385818}.; ",{"$nulls":4},"p.Ser748Ala","c.2242T>G","MODERATE","748/894",19,{"$nulls":5},"5","111","160","84","108","91","116","0","0","0","0.069",{"$nulls":20},"2.004714","2.32","2.785","0.998294","-1.69","0.595","0.082","0.499;0.5",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","107,0","0","107","0/1","141,9","0.06","150",null,"chr10:7172068:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0648"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SH2D2A","chr1:156807291","SH2D2A(P363A)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},92,"PASS","Missense",null,-1,null,"FUNCTION: Could be a T-cell-specific adapter protein involved in the control of T-cell activation. May play a role in the CD4-p56- LCK-dependent signal transduction pathway. Could also play an important role in normal and pathological angiogenesis. Could be an adapter protein that facilitates and regulates interaction of KDR with effector proteins important to endothelial cell survival and proliferation.; ","level2",{"$nulls":3},"p.Pro363Ala","c.1087C>G","MODERATE","363/399",8,{"$nulls":5},"1",{"$nulls":30},"-0.385852","0.46;0.51;0.93",".;1.67;.","1","-1.26;-1.26;-1.46",".;0.243;0.356","0.005;0.005;0.007","0.162;0.152;0.168",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kVEGF",{"$nulls":3},"0/0","212,0","0","213","0/1","223,12","0.0506","237",null,"chr1:156807291:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0506"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SH3BP5L","chr1:248816568","SH3BP5L(R114Q)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs759773883",6.058e-05,{"$nulls":6},"p.Arg114Gln","c.341G>A","MODERATE","114/393",4,{"$nulls":5},"2","389","535",{"$nulls":4},"0.0026","0.0026",{"$nulls":22},"4.18546",null,"3.2","1","-3.44","1.0","0.003","0.869",{"$nulls":3},"ExAC_SAS_AF",6.058e-05,{"$nulls":7},"0/0","370,2","0.0054","372","0/1","460,56","0.1085","516",null,"chr1:248816568:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SH3KBP1","chrX:19550038","SH3KBP1(S477I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Adapter protein involved in regulating diverse signal transduction pathways. Involved in the regulation of endocytosis and lysosomal degradation of ligand-induced receptor tyrosine kinases, including EGFR and MET/hepatocyte growth factor receptor, through an association with CBL and endophilins. The association with CBL, and thus the receptor internalization, may inhibited by an interaction with PDCD6IP and/or SPRY2. Involved in regulation of ligand-dependent endocytosis of the IgE receptor. Attenuates phosphatidylinositol 3-kinase activity by interaction with its regulatory subunit (By similarity). May be involved in regulation of cell adhesion; promotes the interaction between TTK2B and PDCD6IP. May be involved in the regulation of cellular stress response via the MAPK pathways through its interaction with MAP3K4. Is involved in modulation of tumor necrosis factor mediated apoptosis. Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape and migration. {ECO:0000250, ECO:0000269|PubMed:11894095, ECO:0000269|PubMed:11894096, ECO:0000269|PubMed:12177062, ECO:0000269|PubMed:12734385, ECO:0000269|PubMed:12771190, ECO:0000269|PubMed:15090612, ECO:0000269|PubMed:15707590, ECO:0000269|PubMed:16177060, ECO:0000269|PubMed:16256071, ECO:0000269|PubMed:21834987}.; ",{"$nulls":4},"p.Ser477Ile","c.1430G>T","MODERATE","477/665",14,{"$nulls":5},"4","427","364","283","242","401","336","0","0","0","0.128",{"$nulls":20},"2.7336169999999997","1.38","2.525;.;.;.","0.998838","-2.59;-3.3;-2.85;-2.66","0.868;.;.;.","0.057;0.079;0.056;0.048","0.404;0.539;0.463;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1845903","0/0","412,0","0","412","0/1","303,46","0.1318","349",null,"chrX:19550038:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1198"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SHH","chr7:155803111","SHH(A393V)",{"$nulls":6},255,"PASS","Missense","rs751239867",-1,"DISEASE: Microphthalmia, isolated, with coloboma, 5 (MCOPCB5) [MIM:611638]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269|PubMed:12503095}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Holoprosencephaly 3 (HPE3) [MIM:142945]: A structural anomaly of the brain, in which the developing forebrain fails to correctly separate into right and left hemispheres. Holoprosencephaly is genetically heterogeneous and associated with several distinct facies and phenotypic variability. The majority of holoprosencephaly type 3 cases are apparently sporadic, although clear examples of autosomal dominant inheritance have been described. {ECO:0000269|PubMed:10441331, ECO:0000269|PubMed:10556296, ECO:0000269|PubMed:11479728, ECO:0000269|PubMed:15107988, ECO:0000269|PubMed:15221788, ECO:0000269|PubMed:15942952, ECO:0000269|PubMed:15942953, ECO:0000269|PubMed:16282375, ECO:0000269|PubMed:17001669, ECO:0000269|PubMed:19603532, ECO:0000269|PubMed:8896572, ECO:0000269|PubMed:9302262}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Solitary median maxillary central incisor (SMMCI) [MIM:147250]: Rare dental anomaly characterized by the congenital absence of one maxillary central incisor. {ECO:0000269|PubMed:11471164, ECO:0000269|PubMed:15103725}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Triphalangeal thumb-polysyndactyly syndrome (TPTPS) [MIM:174500]: Autosomal dominant syndrome. It is characterized by a wide spectrum of pre- and post-axial abnormalities due to altered SHH expression pattern during limb development. {ECO:0000269|PubMed:12837695, ECO:0000269|PubMed:18417549}. Note=The gene represented in this entry is involved in disease pathogenesis. Mutations located in intron 5 of LMBR1 disrupt a long-range, cis-regulatory element of SHH expression.; DISEASE: Preaxial polydactyly 2 (PPD2) [MIM:174500]: Polydactyly consists of duplication of the distal phalanx. The thumb in PPD2 is usually opposable and possesses a normal metacarpal. {ECO:0000269|PubMed:12837695}. Note=The gene represented in this entry is involved in disease pathogenesis. Mutations located in intron 5 of LMBR1 disrupt a long-range, cis-regulatory element of SHH and result in abnormal, ectopic SHH expression with pathological consequences (PubMed:12837695). {ECO:0000269|PubMed:12837695}.; DISEASE: Hypoplasia or aplasia of tibia with polydactyly (THYP) [MIM:188740]: An autosomal dominant disease characterized by hypoplastic or absent tibia, and polydactyly. {ECO:0000269|PubMed:19847792, ECO:0000269|PubMed:24965254}. Note=The gene represented in this entry is involved in disease pathogenesis. Mutations located in intron 5 of LMBR1 disrupt a long-range, cis-regulatory element of SHH and result in abnormal, ectopic SHH expression with pathological consequences. {ECO:0000303|PubMed:19847792, ECO:0000303|PubMed:24965254}.; DISEASE: Laurin-Sandrow syndrome (LSS) [MIM:135750]: A rare autosomal dominant disorder characterized by polysyndactyly of hands and/or feet, mirror image duplication of the feet, nasal defects, and loss of identity between fibula and tibia. Some patients do not have nasal abnormalities (segmental Laurin-Sandrow syndrome). {ECO:0000269|PubMed:24456159}. Note=The gene represented in this entry is involved in disease pathogenesis. Abnormal SHH limb expression with pathological consequences is caused by duplications (16-75 kb) involving the ZPA regulatory sequence (ZRS), a SHH long-range cis-regulatory element, located in LMBR1 intron 5 (PubMed:24456159).; ","FUNCTION: Sonic hedgehog protein: The C-terminal part of the sonic hedgehog protein precursor displays an autoproteolysis and a cholesterol transferase activity (By similarity). Both activities result in the cleavage of the full-length protein into two parts (ShhN and ShhC) followed by the covalent attachment of a cholesterol moiety to the C-terminal of the newly generated ShhN (By similarity). Both activities occur in the reticulum endoplasmic (By similarity). Once cleaved, ShhC is degraded in the endoplasmic reticulum (By similarity). {ECO:0000250|UniProtKB:Q62226}.; ","level2",{"$nulls":3},"p.Ala393Val","c.1178C>T","MODERATE","393/462",3,{"$nulls":5},"5","308","311","269","269","218","225","0","0","0","0.1556",{"$nulls":20},"1.464743","-5.68","2.095","1","-0.9","0.189","0.147","0.062",{"$nulls":3},"Unknown",-1,"AD","Holoprosencephaly 3; Microphthalmia with coloboma 5 ","Craniofacial; Endocrine; Neurologic; Ophthalmologic","kCANCER,kHEDGEHOG,vGLI",null,null,"C1840235| C1840235| C0266484| C1840529| C1968843","0/0","306,0","0","306","0/1","261,49","0.1581","310",null,"chr7:155803111:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1561"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SHPK","chr17:3615402","SHPK(S320L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Sedoheptulokinase deficiency (SHPKD) [MIM:617213]: An autosomal recessive metabolic disease characterized by increased urinary erythritol and sedoheptulose. Neonatal cholestasis, hypoglycemia, anemia, congenital arthrogryposis multiplex, multiple contractures and dysmorphisms have been reported in SHPKD patients, but the relationship of these features to the SHPKD is unclear. {ECO:0000269|PubMed:25647543}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a modulator of macrophage activation through control of glucose metabolism. {ECO:0000250}.; ",{"$nulls":4},"p.Ser320Leu","c.959C>T","MODERATE","320/478",6,{"$nulls":5},"4","941","737","664","527","814","627","0","0","0","0.1643",{"$nulls":20},"3.800147","1.7",null,"0.999999","-4.9",null,"0.003","0.919",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1291373","0/0","882,0","0","882","0/1","588,109","0.1564","697",null,"chr17:3615402:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1651"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SHPK","chr17:3615402","SHPK(S320L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Sedoheptulokinase deficiency (SHPKD) [MIM:617213]: An autosomal recessive metabolic disease characterized by increased urinary erythritol and sedoheptulose. Neonatal cholestasis, hypoglycemia, anemia, congenital arthrogryposis multiplex, multiple contractures and dysmorphisms have been reported in SHPKD patients, but the relationship of these features to the SHPKD is unclear. {ECO:0000269|PubMed:25647543}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a modulator of macrophage activation through control of glucose metabolism. {ECO:0000250}.; ",{"$nulls":4},"p.Ser320Leu","c.959C>T","MODERATE","320/478",6,{"$nulls":5},"4","941","997","664","727","810","868","0","0","0","0.076",{"$nulls":20},"3.800147","1.7",null,"0.999999","-4.9",null,"0.003","0.919",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1291373","0/0","899,0","0","899","0/1","874,73","0.0771","947",null,"chr17:3615402:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0743"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SIPA1L3","chr19:38162290","SIPA1L3(Sequence Feature)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,"DISEASE: Note=A chromosomal translocation involving SIPA1L3 is found in a patient with bilateral severe ocular abnormalities including congenital cataracts, corneal clouding, iridocorneal and lenticular adhesions and microphthalmia. Chromosomal translocation t(2;19)(q37.3;q13.1). In addition to translocation, missense variant has been found in patient with bilateral congenital cataracts (PubMed:26231217). {ECO:0000269|PubMed:26231217}.; DISEASE: Cataract 45 (CTRCT45) [MIM:616851]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. {ECO:0000269|PubMed:25804400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a critical role in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization in the lens (PubMed:26231217). {ECO:0000269|PubMed:26231217}.; ",{"$nulls":5},"c.3699A>G","MODERATE",null,14,{"$nulls":5},"5","579","590","418","420","502","505","0","0","0","0.1267",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C4225182","0/0","560,0","0","560","0/1","485,67","0.1214","552",null,"chr19:38162290:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1214"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SIPA1L3","chr19:38162290","SIPA1L3(Sequence Feature)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,"DISEASE: Note=A chromosomal translocation involving SIPA1L3 is found in a patient with bilateral severe ocular abnormalities including congenital cataracts, corneal clouding, iridocorneal and lenticular adhesions and microphthalmia. Chromosomal translocation t(2;19)(q37.3;q13.1). In addition to translocation, missense variant has been found in patient with bilateral congenital cataracts (PubMed:26231217). {ECO:0000269|PubMed:26231217}.; DISEASE: Cataract 45 (CTRCT45) [MIM:616851]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. {ECO:0000269|PubMed:25804400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a critical role in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organization in the lens (PubMed:26231217). {ECO:0000269|PubMed:26231217}.; ",{"$nulls":5},"c.3699A>G","MODERATE",null,14,{"$nulls":5},"5","579","598","418","432","499","523","0","0","0","0.0918",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C4225182","0/0","559,0","0","559","0/1","529,49","0.0848","578",null,"chr19:38162290:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0833"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLC18A3","chr10:49611581","SLC18A3(P281T)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in acetylcholine transport into synaptic vesicles. {ECO:0000269|PubMed:8071310}.; ",{"$nulls":4},"p.Pro281Thr","c.841C>A","MODERATE","281/532",1,{"$nulls":5},"5","414","539","351","453","354","462","0","0","0","0.0671",{"$nulls":20},"3.784628","-1.47","2.055","1","-6.96","0.995","0.018","0.763",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the vesicular amine transporter family. The encoded transmembrane protein transports acetylcholine into secretory vesicles for release into the extracellular space. Acetylcholine transport utilizes a proton gradient established by a vacuolar ATPase. This gene is located within the first intron of the choline acetyltransferase gene. [provided by RefSeq, Jul 2008].  ",null,"C4310654","0/0","406,0","0","406","0/1","501,32","0.06","533",null,"chr10:49611581:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0662"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLC1A7","chr1:53103468","SLC1A7(G192A)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transports L-glutamate; the L-glutamate uptake is sodium- and voltage-dependent and chloride-independent. Its associated chloride conductance may participate in visual processing.; ",{"$nulls":4},"p.Gly192Ala","c.575G>C","MODERATE","192/619",5,{"$nulls":5},"4","397","436","280","308","350","381","0","0","0","0.147",{"$nulls":20},"1.957503",".;0.78;.",".;1.58;.","0.999998",".;-2.03;.",".;0.0;.",".;0.489;.","0.506;0.403;0.385",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","380,0","0","380","0/1","357,67","0.158","424",null,"chr1:53103468:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1429"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLC1A7","chr1:53103468","SLC1A7(G192A)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transports L-glutamate; the L-glutamate uptake is sodium- and voltage-dependent and chloride-independent. Its associated chloride conductance may participate in visual processing.; ",{"$nulls":4},"p.Gly192Ala","c.575G>C","MODERATE","192/619",5,{"$nulls":5},"4","397","438","280","333","349","375","0","0","0","0.0613",{"$nulls":20},"1.957503",".;0.78;.",".;1.58;.","0.999998",".;-2.03;.",".;0.0;.",".;0.489;.","0.506;0.403;0.385",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","379,0","0","379","0/1","389,26","0.0627","415",null,"chr1:53103468:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0751"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLC4A5","chr2:74255886","SLC4A5(S305C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates sodium- and bicarbonate-dependent electrogenic sodium bicarbonate cotransport, with a Na(+):HCO3(-) stoichiometry of 2:1. May have a housekeeping function in regulating the pH of tissues in which it is expressed. May play a role in mediating Na(+):HCO3(-) cotransport in hepatocytes and intrahepatic cholangiocytes. Also may be important in protecting the renal paranchyma from alterations in urine pH. {ECO:0000250|UniProtKB:Q6RI88, ECO:0000269|PubMed:11788353, ECO:0000269|PubMed:11997242, ECO:0000269|PubMed:12388414}.; ","gedi",{"$nulls":3},"p.Ser305Cys","c.914C>G","MODERATE","305/1137",10,{"$nulls":5},"5","822","944","551","610","776","882","0","0","0","0.1213",{"$nulls":20},"4.202314","-0.53","2.635;2.635;2.635;.;2.635;2.635","0.999998","-4.29;-4.27;-4.29;-4.42;-4.29;-4.16","0.393;0.393;0.995;0.043;0.077;0.995","0.02;0.018;0.046;0.017;0.046;0.02","0.853;0.853;0.847;0.834;0.871;0.848",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","767,0","0","767","0/1","776,111","0.1251","887",null,"chr2:74255886:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1213"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLC4A5","chr2:74255886","SLC4A5(S305C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates sodium- and bicarbonate-dependent electrogenic sodium bicarbonate cotransport, with a Na(+):HCO3(-) stoichiometry of 2:1. May have a housekeeping function in regulating the pH of tissues in which it is expressed. May play a role in mediating Na(+):HCO3(-) cotransport in hepatocytes and intrahepatic cholangiocytes. Also may be important in protecting the renal paranchyma from alterations in urine pH. {ECO:0000250|UniProtKB:Q6RI88, ECO:0000269|PubMed:11788353, ECO:0000269|PubMed:11997242, ECO:0000269|PubMed:12388414}.; ","gedi",{"$nulls":3},"p.Ser305Cys","c.914C>G","MODERATE","305/1137",10,{"$nulls":5},"5","822","992","551","661","775","933","0","0","0","0.0793",{"$nulls":20},"4.202314","-0.53","2.635;2.635;2.635;.;2.635;2.635","0.999998","-4.29;-4.27;-4.29;-4.42;-4.29;-4.16","0.393;0.393;0.995;0.043;0.077;0.995","0.02;0.018;0.046;0.017;0.046;0.02","0.853;0.853;0.847;0.834;0.871;0.848",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","768,0","0","768","0/1","862,72","0.0771","934",null,"chr2:74255886:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0787"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLC5A2","chr16:31487398","SLC5A2(Y218C)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Renal glucosuria (GLYS) [MIM:233100]: A disorder characterized by persistent isolated glucosuria, normal fasting serum glucose concentration, decreased renal tubular resorption of glucose from the urine, and absence of any other signs of tubular dysfunction. {ECO:0000269|PubMed:14614622}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sodium-dependent glucose transporter. Has a Na(+) to glucose coupling ratio of 1:1.; ",{"$nulls":4},"p.Tyr218Cys","c.653A>G","MODERATE","218/672",6,{"$nulls":5},"5","282","326","222","244","244","291","0","0","0","0.1478",{"$nulls":20},"5.319152","-2.34","2.67","1","-4.04","0.999","0.019","0.473",{"$nulls":3},"Unknown",-1,"AD/AR","Renal glucosuria","Renal",null,"This gene encodes a member of the sodium glucose cotransporter family which are sodium-dependent glucose transport proteins. The encoded protein is the major cotransporter involved in glucose reabsorption in the kidney. Mutations in this gene are associated with renal glucosuria. [provided by RefSeq, Sep 2009].  ",null,"C0017980","0/0","276,0","0","276","0/1","271,48","0.1505","319",null,"chr16:31487398:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1516"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLC5A2","chr16:31487398","SLC5A2(Y218C)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Renal glucosuria (GLYS) [MIM:233100]: A disorder characterized by persistent isolated glucosuria, normal fasting serum glucose concentration, decreased renal tubular resorption of glucose from the urine, and absence of any other signs of tubular dysfunction. {ECO:0000269|PubMed:14614622}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sodium-dependent glucose transporter. Has a Na(+) to glucose coupling ratio of 1:1.; ",{"$nulls":4},"p.Tyr218Cys","c.653A>G","MODERATE","218/672",6,{"$nulls":5},"5","282","364","222","271","244","319","0","0","0","0.0752",{"$nulls":20},"5.319152","-2.34","2.67","1","-4.04","0.999","0.019","0.473",{"$nulls":3},"Unknown",-1,"AD/AR","Renal glucosuria","Renal",null,"This gene encodes a member of the sodium glucose cotransporter family which are sodium-dependent glucose transport proteins. The encoded protein is the major cotransporter involved in glucose reabsorption in the kidney. Mutations in this gene are associated with renal glucosuria. [provided by RefSeq, Sep 2009].  ",null,"C0017980","0/0","280,0","0","280","0/1","326,30","0.0843","356",null,"chr16:31487398:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0738"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLC5A7","chr2:108008548","SLC5A7(L327V)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neuronopathy, distal hereditary motor, 7A (HMN7A) [MIM:158580]: A neuromuscular disorder. Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. HMN7A is characterized by onset in the second decade of progressive distal muscle wasting and weakness affecting the upper and lower limbs and resulting in walking difficulties and hand grip. There is significant muscle atrophy of the hands and lower limbs. The disorder is associated with vocal cord paresis due to involvement of the tenth cranial nerve. {ECO:0000269|PubMed:23141292}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 20, presynaptic (CMS20) [MIM:617143]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness. CMS20 is an autosomal recessive, pre-synaptic form characterized by severe hypotonia and episodic apnea soon after birth, generalized limb fatigability and weakness, delayed walking, ptosis, poor sucking and swallowing. {ECO:0000269|PubMed:27569547}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transmembrane transporter that imports choline from the extracellular space into the neuron with high affinity. Choline uptake is the rate-limiting step in acetylcholine synthesis. Sodium ion- and chloride ion-dependent. {ECO:0000269|PubMed:11027560, ECO:0000269|PubMed:27569547}.; ","tcga-gbm",{"$nulls":3},"p.Leu327Val","c.979C>G","MODERATE","327/580",8,{"$nulls":5},"4","393","478","270","325","359","410","0","0","0","0.0683",{"$nulls":20},"3.583436","-2.67","2.875","1","-3.0","0.998","0.0","0.551;0.56",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310694| C0751882| C1834703","0/0","388,0","0","388","0/1","425,37","0.0801","462",null,"chr2:108008548:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.08"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLC5A7","chr2:108008548","SLC5A7(L327V)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neuronopathy, distal hereditary motor, 7A (HMN7A) [MIM:158580]: A neuromuscular disorder. Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. HMN7A is characterized by onset in the second decade of progressive distal muscle wasting and weakness affecting the upper and lower limbs and resulting in walking difficulties and hand grip. There is significant muscle atrophy of the hands and lower limbs. The disorder is associated with vocal cord paresis due to involvement of the tenth cranial nerve. {ECO:0000269|PubMed:23141292}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myasthenic syndrome, congenital, 20, presynaptic (CMS20) [MIM:617143]: A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness. CMS20 is an autosomal recessive, pre-synaptic form characterized by severe hypotonia and episodic apnea soon after birth, generalized limb fatigability and weakness, delayed walking, ptosis, poor sucking and swallowing. {ECO:0000269|PubMed:27569547}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transmembrane transporter that imports choline from the extracellular space into the neuron with high affinity. Choline uptake is the rate-limiting step in acetylcholine synthesis. Sodium ion- and chloride ion-dependent. {ECO:0000269|PubMed:11027560, ECO:0000269|PubMed:27569547}.; ","tcga-gbm",{"$nulls":3},"p.Leu327Val","c.979C>G","MODERATE","327/580",8,{"$nulls":5},"4","393","486","270","329","360","437","0","0","0","0.0503",{"$nulls":20},"3.583436","-2.67","2.875","1","-3.0","0.998","0.0","0.551;0.56",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310694| C0751882| C1834703","0/0","384,0","0","384","0/1","449,25","0.0527","474",null,"chr2:108008548:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0517"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLC6A19","chr5:1212370","SLC6A19(I183M)",null,null,"topological domain (Extracellular ), sequence variant (In HND; abolishes amino acid transport activity. )",{"$nulls":3},255,"PASS","Missense","rs777423162",-1,"DISEASE: Hyperglycinuria (HG) [MIM:138500]: A condition characterized by excess of glycine in the urine. In some cases it is associated with renal colic and renal oxalate stones. {ECO:0000269|PubMed:19033659}. Note=The disease may be caused by mutations affecting the gene represented in this entry. SLC6A19 deficiency combined with haploinsufficiency of SLC6A20 or partially inactivating mutations in SLC36A2, can be responsible for hyperglycinuria.; DISEASE: Iminoglycinuria (IG) [MIM:242600]: A disorder of renal tubular reabsorption of glycine and imino acids (proline and hydroxyproline), marked by excessive levels of all three substances in the urine. {ECO:0000269|PubMed:19033659}. Note=The disease may be caused by mutations affecting the gene represented in this entry. SLC6A19 deficiency combined with haploinsufficiency of SLC6A20 or partially inactivating mutations in SLC36A2, can be responsible for iminoglycinuria. Additional polymorphisms and mutations in SLC6A18 can contribute to the IG phenotype in some families.; ","FUNCTION: Transporter that mediates resorption of neutral amino acids across the apical membrane of renal and intestinal epithelial cells. This uptake is sodium-dependent and chloride- independent. {ECO:0000269|PubMed:15286788}.; ",{"$nulls":4},"p.Ile183Met","c.549C>G","MODERATE","183/634",4,{"$nulls":5},"4","758","909","534","621","589","714","0","0","0","0.1457",{"$nulls":20},"2.896019","-1.04","2.22","0.805395","-2.07","0.872","0.004","0.549",{"$nulls":3},"Unknown",-1,"AR","Hartnup disease","Biochemical; Dermatologic; Neurologic; Renal",{"$nulls":3},"C0268654| C0018609| C0543541","0/0","704,0","0","704","0/1","746,120","0.1386","866",null,"chr5:1212370:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1353"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLC6A19","chr5:1212370","SLC6A19(I183M)",null,null,"topological domain (Extracellular ), sequence variant (In HND; abolishes amino acid transport activity. )",{"$nulls":3},255,"PASS","Missense","rs777423162",-1,"DISEASE: Hyperglycinuria (HG) [MIM:138500]: A condition characterized by excess of glycine in the urine. In some cases it is associated with renal colic and renal oxalate stones. {ECO:0000269|PubMed:19033659}. Note=The disease may be caused by mutations affecting the gene represented in this entry. SLC6A19 deficiency combined with haploinsufficiency of SLC6A20 or partially inactivating mutations in SLC36A2, can be responsible for hyperglycinuria.; DISEASE: Iminoglycinuria (IG) [MIM:242600]: A disorder of renal tubular reabsorption of glycine and imino acids (proline and hydroxyproline), marked by excessive levels of all three substances in the urine. {ECO:0000269|PubMed:19033659}. Note=The disease may be caused by mutations affecting the gene represented in this entry. SLC6A19 deficiency combined with haploinsufficiency of SLC6A20 or partially inactivating mutations in SLC36A2, can be responsible for iminoglycinuria. Additional polymorphisms and mutations in SLC6A18 can contribute to the IG phenotype in some families.; ","FUNCTION: Transporter that mediates resorption of neutral amino acids across the apical membrane of renal and intestinal epithelial cells. This uptake is sodium-dependent and chloride- independent. {ECO:0000269|PubMed:15286788}.; ",{"$nulls":4},"p.Ile183Met","c.549C>G","MODERATE","183/634",4,{"$nulls":5},"4","758","934","534","647","592","723","0","0","0","0.0622",{"$nulls":20},"2.896019","-1.04","2.22","0.805395","-2.07","0.872","0.004","0.549",{"$nulls":3},"Unknown",-1,"AR","Hartnup disease","Biochemical; Dermatologic; Neurologic; Renal",{"$nulls":3},"C0268654| C0018609| C0543541","0/0","704,0","0","704","0/1","835,55","0.0618","890",null,"chr5:1212370:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0603"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLCO3A1","chr15:92162797","SLCO3A1(S599P)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs753145302",1.5230000000000002E-5,null,"FUNCTION: Mediates the Na(+)-independent transport of organic anions such as estrone-3-sulfate (PubMed:10873595). Mediates transport of prostaglandins (PG) E1 and E2, thyroxine (T4), deltorphin II, BQ-123 and vasopressin, but not DPDPE (a derivative of enkephalin lacking an N-terminal tyrosine residue), estrone-3- sulfate, taurocholate, digoxin nor DHEAS (PubMed:16971491). {ECO:0000269|PubMed:10873595, ECO:0000269|PubMed:16971491}.; ",{"$nulls":4},"p.Ser599Pro","c.1795T>C","MODERATE","599/710",10,{"$nulls":5},"3","554","550",null,null,"461","458","0","0","0","0.2183",{"$nulls":20},"4.199807","-1.49","3.345","1","-2.95;-2.69","0.999;1.0","0.003","0.942;0.95",{"$nulls":3},"ExAC_NFE_AF",1.5230000000000002E-5,{"$nulls":7},"0|0","559,0","0","559","0|1","438,118","0.2122","556",null,"chr15:92162797:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SLCO3A1","chr15:92162797","SLCO3A1(S599P)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs753145302",1.5230000000000002E-5,null,"FUNCTION: Mediates the Na(+)-independent transport of organic anions such as estrone-3-sulfate (PubMed:10873595). Mediates transport of prostaglandins (PG) E1 and E2, thyroxine (T4), deltorphin II, BQ-123 and vasopressin, but not DPDPE (a derivative of enkephalin lacking an N-terminal tyrosine residue), estrone-3- sulfate, taurocholate, digoxin nor DHEAS (PubMed:16971491). {ECO:0000269|PubMed:10873595, ECO:0000269|PubMed:16971491}.; ",{"$nulls":4},"p.Ser599Pro","c.1795T>C","MODERATE","599/710",10,{"$nulls":5},"3","554","604",null,null,"463","501","0","0","0","0.0639",{"$nulls":20},"4.199807","-1.49","3.345","1","-2.95;-2.69","0.999;1.0","0.003","0.942;0.95",{"$nulls":3},"ExAC_NFE_AF",1.5230000000000002E-5,{"$nulls":7},"0|0","543,0","0","543","0|1","544,40","0.0685","584",null,"chr15:92162797:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLCO3A1","chr15:92162797","SLCO3A1(S599P)",null,null,"topological domain (Extracellular )",{"$nulls":3},240,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the Na(+)-independent transport of organic anions such as estrone-3-sulfate (PubMed:10873595). Mediates transport of prostaglandins (PG) E1 and E2, thyroxine (T4), deltorphin II, BQ-123 and vasopressin, but not DPDPE (a derivative of enkephalin lacking an N-terminal tyrosine residue), estrone-3- sulfate, taurocholate, digoxin nor DHEAS (PubMed:16971491). {ECO:0000269|PubMed:10873595, ECO:0000269|PubMed:16971491}.; ",{"$nulls":4},"p.Ser599Pro","c.1795_1797delTCCinsCCA","MODERATE","599/710",10,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","407,0","0","407","0/1","329,91","0.2167","420",null,"chr15:92162797:TCC:CCA",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2167"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SLIT1","chr10:97157824","SLIT1(S136*)",null,null,"repeat (LRR 4 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Thought to act as molecular guidance cue in cellular migration, and function appears to be mediated by interaction with roundabout homolog receptors. During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions (By similarity). SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb. {ECO:0000250}.; ",{"$nulls":4},"p.Ser136*","c.407C>G","HIGH","136/1534",4,{"$nulls":5},"5","229","178","176","133","202","139","0","0","0","0.2662",{"$nulls":5},"(SLIT1|ENSG00000187122|1|1.00)","(SLIT1|ENSG00000187122|1|1.00)",{"$nulls":13},"7.395596",null,null,"1",{"$nulls":3},"0.861;0.875;.;0.869",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","226,0","0","226","0/1","129,43","0.25","172",null,"chr10:97157824:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2331"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SNAP91","chr6:83656754","SNAP91(E220*)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Adaptins are components of the adapter complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Binding of AP180 to clathrin triskelia induces their assembly into 60-70 nm coats (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu220*","c.658G>T","HIGH","220/907",7,{"$nulls":5},"4","87","94","77","89",null,null,"0.0115","0.0115",{"$nulls":7},"(SNAP91|ENSG00000065609|1|1.00)","(SNAP91|ENSG00000065609|1|1.00)",{"$nulls":13},"10.572818999999999",null,null,"1",{"$nulls":3},"0.55;0.548;0.55;0.548;0.548;0.555;0.602;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","86,1","0.0115","87","0/1","77,12","0.1348","89",null,"chr6:83656754:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1348"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SON","chr21:33553001","SON(S1257F)",null,null,"splice variant (In isoform H. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: ZTTK syndrome (ZTTKS) [MIM:617140]: An autosomal dominant syndrome characterized by intellectual disability, developmental delay, malformations of the cerebral cortex, epilepsy, vision problems, musculo-skeletal abnormalities, and congenital malformations. {ECO:0000269|PubMed:25590979, ECO:0000269|PubMed:27256762, ECO:0000269|PubMed:27545676, ECO:0000269|PubMed:27545680}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5'- GA[GT]AN[CG][AG]CC-3'. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680). {ECO:0000269|PubMed:20581448, ECO:0000269|PubMed:21504830, ECO:0000269|PubMed:27545680}.; ",{"$nulls":4},"p.Ser1257Phe","c.3770C>T","MODERATE","1257/2426",3,{"$nulls":5},"4","503","745","386","554","425","591","0","0","0","0.1726",{"$nulls":20},"3.207299","2.28;2.25;2.11","2.19","1;0.723431;0.723431;0.723431;0.723431","-2.29;-2.35;-2.12","0.997;0.998;0.998","0.0;0.0;0.001","0.351;0.349;0.308",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310696","0/0","493,0","0","493","0/1","581,138","0.1919","719",null,"chr21:33553001:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1913"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SON","chr21:33553001","SON(S1257F)",null,null,"splice variant (In isoform H. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: ZTTK syndrome (ZTTKS) [MIM:617140]: An autosomal dominant syndrome characterized by intellectual disability, developmental delay, malformations of the cerebral cortex, epilepsy, vision problems, musculo-skeletal abnormalities, and congenital malformations. {ECO:0000269|PubMed:25590979, ECO:0000269|PubMed:27256762, ECO:0000269|PubMed:27545676, ECO:0000269|PubMed:27545680}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5'- GA[GT]AN[CG][AG]CC-3'. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680). {ECO:0000269|PubMed:20581448, ECO:0000269|PubMed:21504830, ECO:0000269|PubMed:27545680}.; ",{"$nulls":4},"p.Ser1257Phe","c.3770C>T","MODERATE","1257/2426",3,{"$nulls":5},"5","503","618","386","467","426","514","0","0","0","0.1089",{"$nulls":20},"3.207299","2.28;2.25;2.11","2.19","1;0.723431;0.723431;0.723431;0.723431","-2.29;-2.35;-2.12","0.997;0.998;0.998","0.0;0.0;0.001","0.351;0.349;0.308",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310696","0/0","496,0","0","496","0/1","537,70","0.1153","607",null,"chr21:33553001:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1242"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SPATC1","chr8:144040958","SPATC1(A386G)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala386Gly","c.1157C>G","MODERATE","386/591",3,{"$nulls":5},"3",null,null,"665","908","821","1073",null,null,"0","0.5899",{"$nulls":20},"0.735986","0.87;.","0.345","1","-0.76;-0.32","0.231;.","0.372;0.058","0.114;0.12",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","935,0","0","945","0/1","518,737","0.5873","1286",null,"chr8:144040958:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.587"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SPATC1","chr8:144040958","SPATC1(A386G)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala386Gly","c.1157C>G","MODERATE","386/591",3,{"$nulls":5},"3",null,null,"665","912","823","1079",null,null,"0","0.3522",{"$nulls":20},"0.735986","0.87;.","0.345","1","-0.76;-0.32","0.231;.","0.372;0.058","0.114;0.12",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","935,0","0","945","0/1","813,453","0.3578","1293",null,"chr8:144040958:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3421"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SPEF2","chr5:35670211","SPEF2(D503V)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense","rs1030076712",-1,null,"FUNCTION: Required for correct axoneme development in spermatozoa. Important for normal development of the manchette and sperm head morphology. Essential for male fertility. Plays a role in localization of the intraflagellar transport protein IFT20 to the manchette, suggesting function as an adapter for dynein-mediated protein transport during spermatogenesis. Also plays a role in bone growth where it seems to be required for normal osteoblast differentiation. {ECO:0000250|UniProtKB:Q8C9J3}.; ",{"$nulls":4},"p.Asp503Val","c.1508A>T","MODERATE","503/2169",10,{"$nulls":5},"4","171","185","122","121",null,null,"0","0",{"$nulls":22},"4.144875","2.29;2.29;.;3.32;3.32","3.085;.;.;3.085;3.085","1","-7.3;-7.22;.;-6.18;-6.01","1.0;1.0;.;1.0;.","0.0;0.0;.;0.0;0.0","0.931;0.964;.;0.954;0.948",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5231490","0/0","167,0","0","167","0/1","164,18","0.0989","182",null,"chr5:35670211:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0992"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SPEF2","chr5:35670211","SPEF2(D503V)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense","rs1030076712",-1,null,"FUNCTION: Required for correct axoneme development in spermatozoa. Important for normal development of the manchette and sperm head morphology. Essential for male fertility. Plays a role in localization of the intraflagellar transport protein IFT20 to the manchette, suggesting function as an adapter for dynein-mediated protein transport during spermatogenesis. Also plays a role in bone growth where it seems to be required for normal osteoblast differentiation. {ECO:0000250|UniProtKB:Q8C9J3}.; ",{"$nulls":4},"p.Asp503Val","c.1508A>T","MODERATE","503/2169",10,{"$nulls":5},"5","171","169","122","117","153","149","0","0","0","0.0604",{"$nulls":20},"4.144875","2.29;2.29;.;3.32;3.32","3.085;.;.;3.085;3.085","1","-7.3;-7.22;.;-6.18;-6.01","1.0;1.0;.;1.0;.","0.0;0.0;.;0.0;0.0","0.931;0.964;.;0.954;0.948",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5231490","0/0","167,0","0","167","0/1","156,12","0.0714","168",null,"chr5:35670211:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0684"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SRGAP1","chr12:64063065","SRGAP1(R317T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Thyroid cancer, non-medullary, 2 (NMTC2) [MIM:188470]: A form of non-medullary thyroid cancer (NMTC), a cancer characterized by tumors originating from the thyroid follicular cells. NMTCs represent approximately 95% of all cases of thyroid cancer and are classified into papillary, follicular, Hurthle cell, and anaplastic neoplasms. {ECO:0000269|PubMed:23539728}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: GTPase-activating protein for RhoA and Cdc42 small GTPases. Together with CDC42 seems to be involved in the pathway mediating the repulsive signaling of Robo and Slit proteins in neuronal migration. SLIT2, probably through interaction with ROBO1, increases the interaction of SRGAP1 with ROBO1 and inactivates CDC42. {ECO:0000269|PubMed:11672528}.; ",{"$nulls":4},"p.Arg317Thr","c.950G>C","MODERATE","317/1085",7,{"$nulls":5},"5","679","590","480","404","617","516","0","0","0","0.1686",{"$nulls":20},"2.664599","1.03;.;2.61","1.2;.;.","1","-2.88;.;-2.78","0.885;0.04;0.04","0.282;.;0.274","0.536;0.559;0.559",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225426","0/0","643,0","0","643","0/1","459,92","0.167","551",null,"chr12:64063065:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1683"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SRGAP1","chr12:64063065","SRGAP1(R317T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Thyroid cancer, non-medullary, 2 (NMTC2) [MIM:188470]: A form of non-medullary thyroid cancer (NMTC), a cancer characterized by tumors originating from the thyroid follicular cells. NMTCs represent approximately 95% of all cases of thyroid cancer and are classified into papillary, follicular, Hurthle cell, and anaplastic neoplasms. {ECO:0000269|PubMed:23539728}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: GTPase-activating protein for RhoA and Cdc42 small GTPases. Together with CDC42 seems to be involved in the pathway mediating the repulsive signaling of Robo and Slit proteins in neuronal migration. SLIT2, probably through interaction with ROBO1, increases the interaction of SRGAP1 with ROBO1 and inactivates CDC42. {ECO:0000269|PubMed:11672528}.; ",{"$nulls":4},"p.Arg317Thr","c.950G>C","MODERATE","317/1085",7,{"$nulls":5},"5","679","727","480","500","616","654","0","0","0","0.0734",{"$nulls":20},"2.664599","1.03;.;2.61","1.2;.;.","1","-2.88;.;-2.78","0.885;0.04;0.04","0.282;.;0.274","0.536;0.559;0.559",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225426","0/0","661,0","0","661","0/1","659,54","0.0757","713",null,"chr12:64063065:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.07"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SSTR1","chr14:38209643","SSTR1(R85H)",{"$nulls":3},"topological-domain:Cytoplasmic","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for somatostatin with higher affinity for somatostatin-14 than -28. This receptor is coupled via pertussis toxin sensitive G proteins to inhibition of adenylyl cyclase. In addition it stimulates phosphotyrosine phosphatase and Na(+)/H(+) exchanger via pertussis toxin insensitive G proteins.; ",{"$nulls":4},"p.Arg85His","c.254G>A","MODERATE","85/391",3,1,{"$nulls":4},"4","628","772","516","633","489","613","0","0","0","0.1778",{"$nulls":20},"3.75462","1.01","2.52","0.99938","-3.66","0.883","0.039","0.261",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","620,0","0","620","0/1","621,132","0.1753","753",null,"chr14:38209643:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1801"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SSTR1","chr14:38209643","SSTR1(R85H)",{"$nulls":3},"topological-domain:Cytoplasmic","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for somatostatin with higher affinity for somatostatin-14 than -28. This receptor is coupled via pertussis toxin sensitive G proteins to inhibition of adenylyl cyclase. In addition it stimulates phosphotyrosine phosphatase and Na(+)/H(+) exchanger via pertussis toxin insensitive G proteins.; ",{"$nulls":4},"p.Arg85His","c.254G>A","MODERATE","85/391",3,1,{"$nulls":4},"4","628","781","516","633","488","600","0","0","0","0.0733",{"$nulls":20},"3.75462","1.01","2.52","0.99938","-3.66","0.883","0.039","0.261",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","616,0","0","616","0/1","701,60","0.0788","761",null,"chr14:38209643:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0664"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","STARD13","chr13:33129106","STARD13(S524C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells. {ECO:0000269|PubMed:14697242, ECO:0000269|PubMed:16217026}.; ",{"$nulls":4},"p.Ser524Cys","c.1571C>G","MODERATE","524/1113",5,{"$nulls":5},"5","614","807","479","614","551","700","0","0","0","0.1157",{"$nulls":20},"0.838045","3.15;3.14;3.13;2.99","0.035;.;.;.","1","-2.1;-2.07;-1.86;-2.04","0.001;0.005;.;.","0.037;0.031;0.038;0.052","0.071;0.077;0.072;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","597,0","0","597","0/1","682,89","0.1154","771",null,"chr13:33129106:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1124"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","STARD13","chr13:33129106","STARD13(S524C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: GTPase-activating protein for RhoA, and perhaps for Cdc42. May be involved in regulation of cytoskeletal reorganization, cell proliferation and cell motility. Acts a tumor suppressor in hepatocellular carcinoma cells. {ECO:0000269|PubMed:14697242, ECO:0000269|PubMed:16217026}.; ",{"$nulls":4},"p.Ser524Cys","c.1571C>G","MODERATE","524/1113",5,{"$nulls":5},"5","614","770","479","597","549","687","0","0","0","0.0597",{"$nulls":20},"0.838045","3.15;3.14;3.13;2.99","0.035;.;.;.","1","-2.1;-2.07;-1.86;-2.04","0.001;0.005;.;.","0.037;0.031;0.038;0.052","0.071;0.077;0.072;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","587,0","0","587","0/1","694,43","0.0583","737",null,"chr13:33129106:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0653"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","STARD9","chr15:42691540","STARD9(S3321C)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Microtubule-dependent motor protein required for spindle pole assembly during mitosis. Required to stabilize the pericentriolar material (PCM). {ECO:0000269|PubMed:22153075}.; ",{"$nulls":4},"p.Ser3321Cys","c.9962C>G","MODERATE","3321/4700",23,{"$nulls":5},"4","692","565","512","407","624","506","0","0","0","0.332",{"$nulls":20},"0.826981","-0.33","1.7","1","-2.26",null,null,"0.243",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","657,0","0","657","0/1","358,179","0.3333","537",null,"chr15:42691540:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.312"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","STARD9","chr15:42691540","STARD9(S3321C)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Microtubule-dependent motor protein required for spindle pole assembly during mitosis. Required to stabilize the pericentriolar material (PCM). {ECO:0000269|PubMed:22153075}.; ",{"$nulls":4},"p.Ser3321Cys","c.9962C>G","MODERATE","3321/4700",23,{"$nulls":5},"4","692","722","512","519","625","661","0","0","0","0.1392",{"$nulls":20},"0.826981","-0.33","1.7","1","-2.26",null,null,"0.243",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","664,0","0","664","0/1","587,93","0.1368","680",null,"chr15:42691540:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1445"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","STK32A","chr5:147375111","STK32A(P309S)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro309Ser","c.925C>T","MODERATE","309/407",11,{"$nulls":5},"5","260","252","179","156","231","216","0","0","0","0.125",{"$nulls":20},"3.742626","2.0","3.315;.","1","-7.09;-7.22","1.0","0.005;0.003","0.823;0.824",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","251,0","0","251","0/1","202,33","0.1404","235",null,"chr5:147375111:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1218"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","STK32A","chr5:147375111","STK32A(P309S)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro309Ser","c.925C>T","MODERATE","309/407",11,{"$nulls":5},"5","260","261","179","178","231","226","0","0","0","0.0752",{"$nulls":20},"3.742626","2.0","3.315;.","1","-7.09;-7.22","1.0","0.005;0.003","0.823;0.824",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","252,0","0","252","0/1","231,19","0.076","250",null,"chr5:147375111:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0843"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SULF1","chr8:69638630","SULF1(T805P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Exhibits arylsulfatase activity and highly specific endoglucosamine-6-sulfatase activity. It can remove sulfate from the C-6 position of glucosamine within specific subregions of intact heparin. Diminishes HSPG (heparan sulfate proteoglycans) sulfation, inhibits signaling by heparin-dependent growth factors, diminishes proliferation, and facilitates apoptosis in response to exogenous stimulation.; ",{"$nulls":4},"p.Thr805Pro","c.2413A>C","MODERATE","805/871",20,{"$nulls":5},"5","402","727","311","569","333","608","0","0","0","0.0691",{"$nulls":20},"4.214852","1.85;1.85;1.85;.;1.85","3.115;3.115;3.115;.;3.115","0.966366","-3.19;-3.19;-3.19;.;-3.19","0.985;0.985;0.985;.;0.985","0.008;0.008;0.008;.;0.008","0.523;0.52;0.556;0.55;0.518",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","389,0","0","389","0/1","656,50","0.0708","706",null,"chr8:69638630:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0685"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SV2B","chr15:91292432","SV2B(I644M)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably plays a role in the control of regulated secretion in neural and endocrine cells. {ECO:0000250}.; ",{"$nulls":4},"p.Ile644Met","c.1932C>G","MODERATE","644/683",12,{"$nulls":5},"5","542","548","378","374","463","469","0","0","0","0.1557",{"$nulls":20},"3.109495","0.2",".;2.43;2.43","0.999998;0.999999;0.999999","-1.6;-1.5;-1.5",".;1.0;1.0","0.006;0.004;0.004","0.887;0.832;0.832",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","484,0","0","484","0/1","434,71","0.1406","505",null,"chr15:91292432:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1417"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SYNE1","chr6:152164259","SYNE1(R7898S)",null,null,"topological domain (Cytoplasmic ), repeat (Spectrin 69 ), coiled-coil region , splice variant (In isoform 5. ), splice variant (In isoform 6. ), splice variant (In isoform 10. ), splice variant (In isoform GSRP-56. ), splice variant (In isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia, autosomal recessive, 8 (SCAR8) [MIM:610743]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR8 is an autosomal recessive form. {ECO:0000269|PubMed:17159980}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Emery-Dreifuss muscular dystrophy 4, autosomal dominant (EDMD4) [MIM:612998]: A form of Emery-Dreifuss muscular dystrophy, a degenerative myopathy characterized by weakness and atrophy of muscle without involvement of the nervous system, early contractures of the elbows, Achilles tendons and spine, and cardiomyopathy associated with cardiac conduction defects. {ECO:0000269|PubMed:17761684}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. May be involved in nucleus-centrosome attachment and nuclear migration in neural progenitors implicating LINC complex association with SUN1/2 and probably association with cytoplasmic dynein-dynactin motor complexes; SYNE1 and SYNE2 may act redundantly. Required for centrosome migration to the apical cell surface during early ciliogenesis. May be involved in nuclear remodeling during sperm head formation in spermatogenenis; a probable SUN3:SYNE1/KASH1 LINC complex may tether spermatid nuclei to posterior cytoskeletal structures such as the manchette. {ECO:0000250|UniProtKB:Q6ZWR6, ECO:0000269|PubMed:11792814, ECO:0000269|PubMed:18396275}.; ",{"$nulls":4},"p.Arg7898Ser","c.23694G>C","MODERATE","7898/8797",131,{"$nulls":5},"5","447","418","306","286","418","393","0","0","0","0.3791",{"$nulls":20},"2.637468","0.81;.;0.81;0.81;0.81;0.81;0.81","2.835;.;.;.;.;.;.","0.998743;0.998977;0.998743;0.998977;0.998743;0.998743;0.998743;0.99946","-5.61;.;-5.57;-5.69;-5.61;-5.51;-5.57","0.996;.;.;.;.;.;.","0.001;.;0.001;0.001;0.001;0.001;0.001","0.876;0.791;0.818;.;0.855;.;0.801",{"$nulls":3},"Unknown",-1,"AD/AR","Emery-Dreifuss muscular dystrophy 4, autosomal dominant; Spinocerebellar ataxia, autosomal recessive 8","Cardiovascular; Musculoskeletal",null,"This gene encodes a spectrin repeat containing protein expressed in skeletal and smooth muscle, and peripheral blood lymphocytes, that localizes to the nuclear membrane. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia 8, also referred to as autosomal recessive cerebellar ataxia type 1 or recessive ataxia of Beauce. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008].",null,"C2751807| C1853116| C5193121","0/0","425,0","0","425","0/1","250,150","0.375","400",null,"chr6:152164259:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3776"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","SYNE1","chr6:152164259","SYNE1(R7898S)",null,null,"topological domain (Cytoplasmic ), repeat (Spectrin 69 ), coiled-coil region , splice variant (In isoform 5. ), splice variant (In isoform 6. ), splice variant (In isoform 10. ), splice variant (In isoform GSRP-56. ), splice variant (In isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia, autosomal recessive, 8 (SCAR8) [MIM:610743]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR8 is an autosomal recessive form. {ECO:0000269|PubMed:17159980}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Emery-Dreifuss muscular dystrophy 4, autosomal dominant (EDMD4) [MIM:612998]: A form of Emery-Dreifuss muscular dystrophy, a degenerative myopathy characterized by weakness and atrophy of muscle without involvement of the nervous system, early contractures of the elbows, Achilles tendons and spine, and cardiomyopathy associated with cardiac conduction defects. {ECO:0000269|PubMed:17761684}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. May be involved in nucleus-centrosome attachment and nuclear migration in neural progenitors implicating LINC complex association with SUN1/2 and probably association with cytoplasmic dynein-dynactin motor complexes; SYNE1 and SYNE2 may act redundantly. Required for centrosome migration to the apical cell surface during early ciliogenesis. May be involved in nuclear remodeling during sperm head formation in spermatogenenis; a probable SUN3:SYNE1/KASH1 LINC complex may tether spermatid nuclei to posterior cytoskeletal structures such as the manchette. {ECO:0000250|UniProtKB:Q6ZWR6, ECO:0000269|PubMed:11792814, ECO:0000269|PubMed:18396275}.; ",{"$nulls":4},"p.Arg7898Ser","c.23694G>C","MODERATE","7898/8797",131,{"$nulls":5},"5","447","479","306","316","416","423","0","0","0","0.1277",{"$nulls":20},"2.637468","0.81;.;0.81;0.81;0.81;0.81;0.81","2.835;.;.;.;.;.;.","0.998743;0.998977;0.998743;0.998977;0.998743;0.998743;0.998743;0.99946","-5.61;.;-5.57;-5.69;-5.61;-5.51;-5.57","0.996;.;.;.;.;.;.","0.001;.;0.001;0.001;0.001;0.001;0.001","0.876;0.791;0.818;.;0.855;.;0.801",{"$nulls":3},"Unknown",-1,"AD/AR","Emery-Dreifuss muscular dystrophy 4, autosomal dominant; Spinocerebellar ataxia, autosomal recessive 8","Cardiovascular; Musculoskeletal",null,"This gene encodes a spectrin repeat containing protein expressed in skeletal and smooth muscle, and peripheral blood lymphocytes, that localizes to the nuclear membrane. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia 8, also referred to as autosomal recessive cerebellar ataxia type 1 or recessive ataxia of Beauce. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008].",null,"C2751807| C1853116| C5193121","0/0","430,0","0","430","0/1","400,60","0.1304","460",null,"chr6:152164259:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1424"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","SYNJ1","chr21:32688331","SYNJ1(E315Q)",null,null,"domain (SAC )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Parkinson disease 20, early-onset (PARK20) [MIM:615530]: An early-onset form of Parkinson disease, a complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability, as well as by a clinically significant response to treatment with levodopa. The pathology involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. PARK20 is characterized by young adult-onset of parkinsonism. Additional features may include seizures, cognitive decline, abnormal eye movements, and dystonia. {ECO:0000269|PubMed:23804563, ECO:0000269|PubMed:23804577, ECO:0000269|PubMed:27496670}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 53 (EIEE53) [MIM:617389]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE53 inheritance is autosomal recessive. {ECO:0000269|PubMed:27435091}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Phosphatase that acts on various phosphoinositides, including phosphatidylinositol 4-phosphate, phosphatidylinositol (4,5)-bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate (PubMed:27435091). Has a role in clathrin-mediated endocytosis (By similarity). Hydrolyzes PIP2 bound to actin regulatory proteins resulting in the rearrangement of actin filaments downstream of tyrosine kinase and ASH/GRB2 (By similarity). {ECO:0000250|UniProtKB:O18964, ECO:0000250|UniProtKB:Q62910, ECO:0000269|PubMed:27435091}.; ",{"$nulls":4},"p.Glu315Gln","c.943G>C","MODERATE","315/1612",7,{"$nulls":5},"5","289","422","189","290","256","389","0","0","0","0.054",{"$nulls":20},"3.753636","0.26;0.26;.;0.26;0.26;0.26","2.38;.;.;.;.;.","1","-2.58;-2.56;.;-2.58;-2.56;-2.76","1.0;.;.;1.0;.;.","0.003;0.003;.;0.003;0.017;0.003","0.812;0.821;0.78;0.784;0.782;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011].",null,"C3809824| C4479313","0/0","267,0","0","267","0/1","364,27","0.0691","391",null,"chr21:32688331:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0655"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TACSTD2","chr1:58576467","TACSTD2(I230M)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Corneal dystrophy, gelatinous drop-like (GDLD) [MIM:204870]: A form of lattice corneal dystrophy, a class of inherited stromal amyloidoses characterized by pathognomonic branching lattice figures in the cornea. GDLD is an autosomal recessive disorder characterized by severe corneal amyloidosis leading to blindness. Clinical manifestations, which appear in the first decade of life, include blurred vision, photophobia, and foreign-body sensation. By the third decade, raised, yellowish- gray, gelatinous masses severely impair visual acuity. {ECO:0000269|PubMed:10192395}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May function as a growth factor receptor.; ",{"$nulls":4},"p.Ile230Met","c.690C>G","MODERATE","230/323",1,{"$nulls":5},"4","1485","1621","1166","1236","1247","1386","0.0007","0.0007","0","0.1385",{"$nulls":20},"2.916454","-1.38","1.735","0.969233","-2.02","0.232","0.001","0.168",{"$nulls":3},"Unknown",-1,"AR","Corneal dystrophy, gelatinous drop-like","Ophthalmologic",{"$nulls":3},"C0339273","0/0","1415,1","0.0007","1416","0/1","1343,216","0.1386","1559",null,"chr1:58576467:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1472"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TBC1D8","chr2:101021724","TBC1D8(M928I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).; ",{"$nulls":4},"p.Met928Ile","c.2784G>C","MODERATE","928/1155",17,{"$nulls":5},"4","216","218","143","138","203","201","0","0","0","0.1045",{"$nulls":20},"3.180566","0.96","2.255;.","0.994919","-1.07","0.255;.","0.067;0.064","0.581;0.558",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","214,0","0","214","0/1","191,25","0.1157","216",null,"chr2:101021724:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0942"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TBC1D8","chr2:101021724","TBC1D8(M928I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).; ",{"$nulls":4},"p.Met928Ile","c.2784G>C","MODERATE","928/1155",17,{"$nulls":5},"3","216","255",null,null,"203","242","0","0","0","0.0826",{"$nulls":20},"3.180566","0.96","2.255;.","0.994919","-1.07","0.255;.","0.067;0.064","0.581;0.558",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","214,0","0","214","0/1","226,21","0.085","247",null,"chr2:101021724:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TBL1X","chrX:9711710","TBL1X(F513L)",null,null,"repeat (WD 7 ), sequence variant (In CHNG8. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units (PubMed:14980219). Plays an essential role in transcription activation mediated by nuclear receptors. Probably acts as integral component of corepressor complexes that mediates the recruitment of the 19S proteasome complex, leading to the subsequent proteasomal degradation of transcription repressor complexes, thereby allowing cofactor exchange (PubMed:21240272). {ECO:0000269|PubMed:14980219, ECO:0000269|PubMed:21240272}.; ","level2",{"$nulls":3},"p.Phe513Leu","c.1539C>G","MODERATE","513/577",16,{"$nulls":5},"4","587","711","390","494","531","656","0","0","0","0.0534",{"$nulls":20},"2.133454","-0.25;-0.25;-0.25;-0.25;.;.;.;.",".;2.17;.;2.17;2.17;2.17;2.17;.","0.999983","-5.53;-5.54;-5.53;-5.54;.;.;.;.",".;0.971;.;0.971;0.971;0.971;0.971;.","0.002;0.002;0.002;0.002;.;.;.;.","0.616;0.617;0.616;0.619;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kWNT",null,null,"C5231395","0/0","563,0","0","563","0/1","646,42","0.061","688",null,"chrX:9711710:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0628"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TBR1","chr2:161416499","TBR1(S30F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable transcriptional regulator involved in developmental processes. Required for normal brain development.; ",{"$nulls":4},"p.Ser30Phe","c.89C>T","MODERATE","30/682",1,{"$nulls":5},"5","496","777","368","549","433","668","0","0","0","0.1138",{"$nulls":20},"3.161455","-2.31","1.525","0.999654","-0.81","0.41","0.001","0.484",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1853755","0/0","460,0","0","460","0/1","648,88","0.1196","736",null,"chr2:161416499:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1056"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TBR1","chr2:161416499","TBR1(S30F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable transcriptional regulator involved in developmental processes. Required for normal brain development.; ",{"$nulls":4},"p.Ser30Phe","c.89C>T","MODERATE","30/682",1,{"$nulls":5},"5","496","630","368","455","434","541","0","0","0","0.0536",{"$nulls":20},"3.161455","-2.31","1.525","0.999654","-0.81","0.41","0.001","0.484",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1853755","0/0","460,0","0","460","0/1","560,32","0.0541","592",null,"chr2:161416499:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0549"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TBX3","chr12:114682812","TBX3(R130T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional repressor involved in developmental processes. Probably plays a role in limb pattern formation. Acts as a negative regulator of PML function in cellular senescence. {ECO:0000269|PubMed:10468588, ECO:0000269|PubMed:22002537}.; ","gedi",{"$nulls":3},"p.Arg130Thr","c.389G>C","MODERATE","130/743",1,{"$nulls":5},"5","198","166","154","131","158","129","0","0","0","0.2093",{"$nulls":20},"5.231883","-3.3","3.98","1","-5.96","1.0;0.999","0.0","0.899;0.907",{"$nulls":3},"Unknown",-1,"AD","Ulnar-Mammary syndrome","Cardiovascular; Dental; Endocrine; Genitourinary; Musculoskeletal; Renal",{"$nulls":3},"C1866994","0/0","196,0","0","196","0/1","133,29","0.179","162",null,"chr12:114682812:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1985"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TBX3","chr12:114682812","TBX3(R130T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional repressor involved in developmental processes. Probably plays a role in limb pattern formation. Acts as a negative regulator of PML function in cellular senescence. {ECO:0000269|PubMed:10468588, ECO:0000269|PubMed:22002537}.; ","gedi",{"$nulls":3},"p.Arg130Thr","c.389G>C","MODERATE","130/743",1,{"$nulls":5},"5","198","196","154","157","158","163","0","0","0","0.0798",{"$nulls":20},"5.231883","-3.3","3.98","1","-5.96","1.0;0.999","0.0","0.899;0.907",{"$nulls":3},"Unknown",-1,"AD","Ulnar-Mammary syndrome","Cardiovascular; Dental; Endocrine; Genitourinary; Musculoskeletal; Renal",{"$nulls":3},"C1866994","0/0","191,0","0","191","0/1","174,15","0.0794","189",null,"chr12:114682812:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0828"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TEX261","chr2:70993740","TEX261(E36Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu36Gln","c.106G>C","MODERATE","36/196",2,{"$nulls":5},"5","325","365","217","245","308","333","0","0","0","0.1081",{"$nulls":20},"4.3433910000000004",null,".;3.17","1",".;-2.55",".;0.991",".;0.0","0.914",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","318,0","0","318","0/1","315,38","0.1076","353",null,"chr2:70993740:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.098"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TEX261","chr2:70993740","TEX261(E36Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu36Gln","c.106G>C","MODERATE","36/196",2,{"$nulls":5},"4","325","404",null,null,"309","377","0","0","0","0.061",{"$nulls":20},"4.3433910000000004",null,".;3.17","1",".;-2.55",".;0.991",".;0.0","0.914",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","318,0","0","318","0/1","361,24","0.0623","385",null,"chr2:70993740:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TGFB1I1","chr16:31476862","TGFB1I1(G324D)",null,null,"domain (LIM zinc-binding 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. Links various intracellular signaling modules to plasma membrane receptors and regulates the Wnt and TGFB signaling pathways. May also regulate SLC6A3 and SLC6A4 targeting to the plasma membrane hence regulating their activity. In the nucleus, functions as a nuclear receptor coactivator regulating glucocorticoid, androgen, mineralocorticoid and progesterone receptor transcriptional activity. May play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA- binding activity. {ECO:0000269|PubMed:10075738, ECO:0000269|PubMed:11463817, ECO:0000269|PubMed:11856738, ECO:0000269|PubMed:12177201, ECO:0000269|PubMed:12445807, ECO:0000269|PubMed:12700349, ECO:0000269|PubMed:15211577, ECO:0000269|PubMed:15561701, ECO:0000269|PubMed:16141357, ECO:0000269|PubMed:16624805, ECO:0000269|PubMed:16803896, ECO:0000269|PubMed:16849583, ECO:0000269|PubMed:17166536, ECO:0000269|PubMed:17233630, ECO:0000269|PubMed:9032249}.; ",{"$nulls":4},"p.Gly324Asp","c.971G>A","MODERATE","324/461",10,{"$nulls":5},"4","370","381","289","301","252","271","0","0","0","0.1292",{"$nulls":20},"4.835406","-2.19","2.205;.;.;.","1","-6.86","0.999;.;.;.","0.001","0.798;0.847;0.845;0.845",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","345,0","0","345","0/1","319,43","0.1188","362",null,"chr16:31476862:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1096"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TGFB1I1","chr16:31476862","TGFB1I1(G324D)",null,null,"domain (LIM zinc-binding 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. Links various intracellular signaling modules to plasma membrane receptors and regulates the Wnt and TGFB signaling pathways. May also regulate SLC6A3 and SLC6A4 targeting to the plasma membrane hence regulating their activity. In the nucleus, functions as a nuclear receptor coactivator regulating glucocorticoid, androgen, mineralocorticoid and progesterone receptor transcriptional activity. May play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA- binding activity. {ECO:0000269|PubMed:10075738, ECO:0000269|PubMed:11463817, ECO:0000269|PubMed:11856738, ECO:0000269|PubMed:12177201, ECO:0000269|PubMed:12445807, ECO:0000269|PubMed:12700349, ECO:0000269|PubMed:15211577, ECO:0000269|PubMed:15561701, ECO:0000269|PubMed:16141357, ECO:0000269|PubMed:16624805, ECO:0000269|PubMed:16803896, ECO:0000269|PubMed:16849583, ECO:0000269|PubMed:17166536, ECO:0000269|PubMed:17233630, ECO:0000269|PubMed:9032249}.; ",{"$nulls":4},"p.Gly324Asp","c.971G>A","MODERATE","324/461",10,{"$nulls":5},"4","370","392","289","318","253","266","0","0","0","0.0752",{"$nulls":20},"4.835406","-2.19","2.205;.;.;.","1","-6.86","0.999;.;.;.","0.001","0.798;0.847;0.845;0.845",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","345,0","0","345","0/1","349,26","0.0693","375",null,"chr16:31476862:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.066"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","THSD7B","chr2:137618431","THSD7B(G1204V)",null,null,"topological domain (Extracellular ), domain (TSP type-1 15 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly1204Val","c.3611G>T","MODERATE","1204/1608",18,{"$nulls":5},"4","468","645","354","482","402","521","0","0","0","0.142",{"$nulls":20},"4.189576","-0.56;.;.",null,"1","-7.64;.;.",null,"0.0;.;.","0.874;0.875;0.904",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","439,0","0","439","0/1","533,81","0.1319","614",null,"chr2:137618431:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.112"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TMEM179B","chr11:62790019","TMEM179B(L211H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu211His","c.632T>A","MODERATE","211/219",5,{"$nulls":5},"4","478","464","322","315","430","421","0","0","0","0.1188",{"$nulls":20},"3.16831",null,"2.255","1;0.522023;1;1","-2.54","1.0","0.001","0.536",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","459,0","0","459","0/1","384,55","0.1253","439",null,"chr11:62790019:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1238"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TMEM211","chr22:24939380","TMEM211(C52*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Cys52*","c.156C>A","HIGH","52/200",1,{"$nulls":5},"4","340","281","256","209","285","230","0","0","0","0.1217",{"$nulls":5},"(TMEM211|ENSG00000206069|1|1.00)","(TMEM211|ENSG00000206069|1|1.00)",{"$nulls":13},"0.100645",null,null,"1;0.999714",{"$nulls":3},".;0.266",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","337,0","0","337","0/1","245,30","0.1091","275",null,"chr22:24939380:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0909"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TMEM211","chr22:24939380","TMEM211(C52*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Cys52*","c.156C>A","HIGH","52/200",1,{"$nulls":5},"4","340","373","256","274","285","314","0","0","0","0.0701",{"$nulls":5},"(TMEM211|ENSG00000206069|1|1.00)","(TMEM211|ENSG00000206069|1|1.00)",{"$nulls":13},"0.100645",null,null,"1;0.999714",{"$nulls":3},".;0.266",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","337,0","0","337","0/1","341,24","0.0658","365",null,"chr22:24939380:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.062"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TMEM247","chr2:46480669","TMEM247(R140_Q152dup)",{"$nulls":6},249,"PASS","Inframe Indel","rs879814156",-1,{"$nulls":6},"p.Arg140_Gln152dup","c.419_457dupGGGAGCGGCAGCACGAGGTGGTGATGGAGCAGCTGCAGC","MODERATE","153/218",2,{"$nulls":5},"1",{"$nulls":41},"Unknown",-1,{"$nulls":7},"0/0","256,0","0","303","0/1","83,218","0.5767","378",null,"chr2:46480669:C:CAGCGGCAGCACGAGGTGGTGATGGAGCAGCTGCAGCGGG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.5767"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TNIK","chr3:171084186","TNIK(F1046L)",null,null,"region of interest (Mediates interaction with NEDD4 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Mental retardation, autosomal recessive 54 (MRT54) [MIM:617028]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT54 patients manifest intellectual disability, delayed speech and hyperactivity. {ECO:0000269|PubMed:27106596}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine kinase that acts as an essential activator of the Wnt signaling pathway. Recruited to promoters of Wnt target genes and required to activate their expression. May act by phosphorylating TCF4/TCF7L2. Appears to act upstream of the JUN N-terminal pathway. May play a role in the response to environmental stress. Part of a signaling complex composed of NEDD4, RAP2A and TNIK which regulates neuronal dendrite extension and arborization during development. More generally, it may play a role in cytoskeletal rearrangements and regulate cell spreading. Phosphorylates SMAD1 on Thr-322. {ECO:0000269|PubMed:10521462, ECO:0000269|PubMed:15342639, ECO:0000269|PubMed:19061864, ECO:0000269|PubMed:19816403, ECO:0000269|PubMed:20159449, ECO:0000269|PubMed:21690388}.; ",{"$nulls":4},"p.Phe1046Leu","c.3138C>G","MODERATE","1046/1360",26,{"$nulls":5},"5","392","552","305","422","247","342","0","0","0","0.1813",{"$nulls":20},"4.079618","-2.85;-2.8;-2.84;-2.79;-2.84;-2.86;-2.88;-2.82","3.32;.;.;.;.;.;.;.","1","-5.5;-5.49;-5.5;-5.49;-5.5;-5.6;-5.6;-5.5","0.99;0.954;0.994;0.954;0.94;0.954;0.954;0.94","0.0","0.91;0.893;0.934;0.909;0.865;0.891;0.928;0.908",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310755","0/0","356,1","0.0028","357","0/1","423,74","0.1489","497",null,"chr3:171084186:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1398"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TNIK","chr3:171084186","TNIK(F1046L)",null,null,"region of interest (Mediates interaction with NEDD4 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Mental retardation, autosomal recessive 54 (MRT54) [MIM:617028]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT54 patients manifest intellectual disability, delayed speech and hyperactivity. {ECO:0000269|PubMed:27106596}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine kinase that acts as an essential activator of the Wnt signaling pathway. Recruited to promoters of Wnt target genes and required to activate their expression. May act by phosphorylating TCF4/TCF7L2. Appears to act upstream of the JUN N-terminal pathway. May play a role in the response to environmental stress. Part of a signaling complex composed of NEDD4, RAP2A and TNIK which regulates neuronal dendrite extension and arborization during development. More generally, it may play a role in cytoskeletal rearrangements and regulate cell spreading. Phosphorylates SMAD1 on Thr-322. {ECO:0000269|PubMed:10521462, ECO:0000269|PubMed:15342639, ECO:0000269|PubMed:19061864, ECO:0000269|PubMed:19816403, ECO:0000269|PubMed:20159449, ECO:0000269|PubMed:21690388}.; ",{"$nulls":4},"p.Phe1046Leu","c.3138C>G","MODERATE","1046/1360",26,{"$nulls":5},"5","392","532","305","397","249","328","0","0","0","0.0732",{"$nulls":20},"4.079618","-2.85;-2.8;-2.84;-2.79;-2.84;-2.86;-2.88;-2.82","3.32;.;.;.;.;.;.;.","1","-5.5;-5.49;-5.5;-5.49;-5.5;-5.6;-5.6;-5.5","0.99;0.954;0.994;0.954;0.94;0.954;0.954;0.94","0.0","0.91;0.893;0.934;0.909;0.865;0.891;0.928;0.908",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310755","0/0","354,0","0","354","0/1","455,26","0.0541","481",null,"chr3:171084186:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0529"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TNNI3K","chr1:74249464","TNNI3K(D52A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Cardiac conduction disease with or without dilated cardiomyopathy (CCDD) [MIM:616117]: A cardiac disorder characterized by atrial tachyarrhythmia and conduction system disease. Some patients have dilated cardiomyopathy. {ECO:0000269|PubMed:24925317}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May play a role in cardiac physiology. {ECO:0000303|PubMed:12721663}.; ",{"$nulls":4},"p.Asp52Ala","c.155A>C","MODERATE","52/835",3,{"$nulls":5},"5","370","429","289","328","305","335","0","0","0","0.1284",{"$nulls":20},"2.846228",".;-0.83;-0.54;-0.82",".;.;.;1.7","0.999988;0.999991",".;-0.78;-0.08;-1.47",".;.;.;0.817",".;0.006;0.003;0.004","0.697;0.669;0.771;0.693",{"$nulls":3},"Unknown",-1,"AD","Cardiac conduction disease with or without dilated cardiomyopathy","Cardiovascular",null,"This gene encodes a protein that belongs to the MAP kinase kinase kinase (MAPKKK) family of protein kinases. The protein contains ankyrin repeat, protein kinase and serine-rich domains and is thought to play a role in cardiac physiology. [provided by RefSeq, Sep 2012].  ",null,"C4015285","0/0","362,0","0","362","0/1","374,44","0.1053","418",null,"chr1:74249464:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1098"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TNNI3K","chr1:74249464","TNNI3K(D52A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Cardiac conduction disease with or without dilated cardiomyopathy (CCDD) [MIM:616117]: A cardiac disorder characterized by atrial tachyarrhythmia and conduction system disease. Some patients have dilated cardiomyopathy. {ECO:0000269|PubMed:24925317}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May play a role in cardiac physiology. {ECO:0000303|PubMed:12721663}.; ",{"$nulls":4},"p.Asp52Ala","c.155A>C","MODERATE","52/835",3,{"$nulls":5},"5","370","505","289","372","306","407","0","0","0","0.0737",{"$nulls":20},"2.846228",".;-0.83;-0.54;-0.82",".;.;.;1.7","0.999988;0.999991",".;-0.78;-0.08;-1.47",".;.;.;0.817",".;0.006;0.003;0.004","0.697;0.669;0.771;0.693",{"$nulls":3},"Unknown",-1,"AD","Cardiac conduction disease with or without dilated cardiomyopathy","Cardiovascular",null,"This gene encodes a protein that belongs to the MAP kinase kinase kinase (MAPKKK) family of protein kinases. The protein contains ankyrin repeat, protein kinase and serine-rich domains and is thought to play a role in cardiac physiology. [provided by RefSeq, Sep 2012].  ",null,"C4015285","0/0","364,0","0","364","0/1","468,33","0.0659","501",null,"chr1:74249464:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0726"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TP53","chr17:7675218","TP53(K93E)",null,null,"region of interest (Interaction with CCAR2 ), region of interest (Interaction with WWOX ), splice variant (In isoform 7, isoform 8 and isoform 9. ), sequence variant (In a sporadic cancer; somatic mutation. TP53(L93M)), sequence variant (In a sporadic cancer; somatic mutation. TP53(L93P))",{"$nulls":3},255,"PASS","Missense","rs747342068",1.5090000000000001E-5,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Lys93Glu","c.277A>G","MODERATE","93/410",5,34,{"$nulls":4},"4","302","269","223","189","285","234","0","0","0","0.359",{"$nulls":20},"4.398475","-7.19;-7.19;.;-7.19;.;.;-7.19;-7.19;.;.;-7.19;.;.;-7.19;-7.19",".;.;.;3.265;.;3.265;3.265;3.265;.;.;3.265;.;.;.;.","1","-3.59;-3.71;.;-3.89;.;.;-3.71;-3.71;.;.;-3.89;.;.;-3.58;-3.62","1.0;.;.;1.0;.;1.0;0.991;1.0;.;.;1.0;.;.;0.999;.","0.003;0.003;.;0.0;.;.;0.003;0.003;.;.;0.0;.;.;0.022;0.001","0.97;0.967;0.974;0.973;0.974;0.968;0.97;0.968;0.965;0.878;0.975;0.974;0.935;.;.",{"$nulls":3},"ExAC_NFE_AF",1.5090000000000001E-5,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","298,0","0","298","0/1","160,105","0.3962","265",null,"chr17:7675218:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3598"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TP53","chr17:7675218","TP53(K93E)",null,null,"region of interest (Interaction with CCAR2 ), region of interest (Interaction with WWOX ), splice variant (In isoform 7, isoform 8 and isoform 9. ), sequence variant (In a sporadic cancer; somatic mutation. TP53(L93M)), sequence variant (In a sporadic cancer; somatic mutation. TP53(L93P))",{"$nulls":3},255,"PASS","Missense","rs747342068",1.5090000000000001E-5,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Lys93Glu","c.277A>G","MODERATE","93/410",5,34,{"$nulls":4},"3","302","329",null,null,"285","294","0","0","0","0.1497",{"$nulls":20},"4.398475","-7.19;-7.19;.;-7.19;.;.;-7.19;-7.19;.;.;-7.19;.;.;-7.19;-7.19",".;.;.;3.265;.;3.265;3.265;3.265;.;.;3.265;.;.;.;.","1","-3.59;-3.71;.;-3.89;.;.;-3.71;-3.71;.;.;-3.89;.;.;-3.58;-3.62","1.0;.;.;1.0;.;1.0;0.991;1.0;.;.;1.0;.;.;0.999;.","0.003;0.003;.;0.0;.;.;0.003;0.003;.;.;0.0;.;.;0.022;0.001","0.97;0.967;0.974;0.973;0.974;0.968;0.97;0.968;0.965;0.878;0.975;0.974;0.935;.;.",{"$nulls":3},"ExAC_NFE_AF",1.5090000000000001E-5,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","298,0","0","298","0/1","269,57","0.1748","326",null,"chr17:7675218:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TPD52L2","chr20:63887595","TPD52L2(P179A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro179Ala","c.535C>G","MODERATE","179/229",7,{"$nulls":5},"4","605","738","407","492","559","673","0","0","0","0.0906",{"$nulls":20},"3.544921","1.2;1.37;1.26;1.39",null,"0.96536;0.984863;0.96536;0.984863;1;1;1","-3.53;-3.79;-3.52;-3.79",".;1.0;.;1.0","0.0;0.033;0.0;0.031","0.772;0.708;0.76;0.685",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","559,0","0","559","0/1","636,64","0.0914","700",null,"chr20:63887595:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0915"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TPD52L2","chr20:63887595","TPD52L2(P179A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro179Ala","c.535C>G","MODERATE","179/229",7,{"$nulls":5},"4","605","753","407","500","558","685","0","0","0","0.0555",{"$nulls":20},"3.544921","1.2;1.37;1.26;1.39",null,"0.96536;0.984863;0.96536;0.984863;1;1;1","-3.53;-3.79;-3.52;-3.79",".;1.0;.;1.0","0.0;0.033;0.0;0.031","0.772;0.708;0.76;0.685",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","557,0","0","557","0/1","663,47","0.0662","710",null,"chr20:63887595:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.062"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TPP2","chr13:102644620","TPP2(D747N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. May be able to complement the 26S proteasome function to some extent under conditions in which the latter is inhibited. Stimulates adipogenesis (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp747Asn","c.2239G>A","MODERATE","747/1262",18,{"$nulls":5},"5","361","366","228","226","337","341","0","0","0","0.1144",{"$nulls":20},"3.022774",null,"1.15;.","1","-1.39","0.001;.","0.249;0.231","0.225;0.249",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","348,0","0","348","0/1","314,43","0.1204","357",null,"chr13:102644620:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.115"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TRAPPC3","chr1:36140127","TRAPPC3(T28S)",null,null,"splice variant (In isoform 2. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi.; ",{"$nulls":4},"p.Thr28Ser","c.82A>T","MODERATE","28/188",2,{"$nulls":5},"2",null,null,"140","164",{"$nulls":26},"2.300404",".;1.16;1.16",".;-0.55;.","1",".;0.74;0.15",".;0.0;.",".;0.403;0.479","0.654;0.715;0.638",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","187,0","0","187","0/1","207,11","0.0505","218",null,"chr1:36140127:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0549"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TRIM51","chr11:55891293","TRIM51(K340N)",null,null,"domain (B30.2/SPRY )",{"$nulls":3},255,"PASS","Missense",null,-1,null,null,"tcga-gbm",{"$nulls":3},"p.Lys340Asn","c.1020A>C","MODERATE","340/452",7,{"$nulls":5},"4","438","542","315","365","387","448","0","0","0","0.1451",{"$nulls":20},"1.837608","-0.74","3.85;.","0.993098;0.995832","-3.25;-3.7","1.0;.","0.003;0.002","0.146;0.161",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","422,0","0","422","0/1","436,78","0.1518","514",null,"chr11:55891293:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1452"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TRIP11","chr14:91975188","TRIP11(R1814M)",null,null,"domain (GRIP ), sequence variant (In ODCD; due to a nucleotide substitution that causes protein truncation or in-frame exon 4 skipping. ), sequence variant (In ACG1A and ODCD. ), sequence variant (In ACG1A. ), sequence variant (In ACG1A. ), sequence variant (In ACG1A; does not localize to cis-Golgi; results in disruption of Golgi cisternal stack architecture. ), sequence variant (In ACG1A. ), sequence variant (In ACG1A. ), sequence variant (In ODCD. )",{"$nulls":3},255,"PASS","Missense","rs768341546",9.61e-05,"DISEASE: Note=A chromosomal aberration involving TRIP11 may be a cause of acute myelogenous leukemia. Translocation t(5;14)(q33;q32) with PDGFRB. The fusion protein may be involved in clonal evolution of leukemia and eosinophilia. {ECO:0000269|PubMed:9373237}.; DISEASE: Achondrogenesis 1A (ACG1A) [MIM:200600]: A form of achondrogenesis type 1, a lethal form of chondrodysplasia characterized by deficient ossification in the lumbar vertebrae and absent ossification in the sacral, pubic and ischial bones and clinically by stillbirth or early death. In addition to severe micromelia, there is a disproportionately large cranium due to marked edema of soft tissues. {ECO:0000269|PubMed:20089971}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds the ligand binding domain of the thyroid receptor (THRB) in the presence of triiodothyronine and enhances THRB- modulated transcription. Golgi auto-antigen; probably involved in maintaining cis-Golgi structure. {ECO:0000269|PubMed:10189370, ECO:0000269|PubMed:9256431}.; ","gedi|level2",{"$nulls":3},"p.Arg1814Met","c.5441G>T","MODERATE","1814/1979",18,{"$nulls":5},"5","610","656","406","441","511","574","0","0","0","0.169",{"$nulls":20},"3.277805","3.65","1.935","0.99999","-2.94","0.996","0.003","0.427",{"$nulls":3},"ExAC_AFR_AF",9.61e-05,"AR","Achondrogenesis, type IA","Musculoskeletal","COSMIC",null,null,"C0265273| C2745953","0/0","596,0","0","596","0/1","536,105","0.1638","641",null,"chr14:91975188:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1542"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TRIP11","chr14:91975188","TRIP11(R1814M)",null,null,"domain (GRIP ), sequence variant (In ODCD; due to a nucleotide substitution that causes protein truncation or in-frame exon 4 skipping. ), sequence variant (In ACG1A and ODCD. ), sequence variant (In ACG1A. ), sequence variant (In ACG1A. ), sequence variant (In ACG1A; does not localize to cis-Golgi; results in disruption of Golgi cisternal stack architecture. ), sequence variant (In ACG1A. ), sequence variant (In ACG1A. ), sequence variant (In ODCD. )",{"$nulls":3},255,"PASS","Missense","rs768341546",9.61e-05,"DISEASE: Note=A chromosomal aberration involving TRIP11 may be a cause of acute myelogenous leukemia. Translocation t(5;14)(q33;q32) with PDGFRB. The fusion protein may be involved in clonal evolution of leukemia and eosinophilia. {ECO:0000269|PubMed:9373237}.; DISEASE: Achondrogenesis 1A (ACG1A) [MIM:200600]: A form of achondrogenesis type 1, a lethal form of chondrodysplasia characterized by deficient ossification in the lumbar vertebrae and absent ossification in the sacral, pubic and ischial bones and clinically by stillbirth or early death. In addition to severe micromelia, there is a disproportionately large cranium due to marked edema of soft tissues. {ECO:0000269|PubMed:20089971}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds the ligand binding domain of the thyroid receptor (THRB) in the presence of triiodothyronine and enhances THRB- modulated transcription. Golgi auto-antigen; probably involved in maintaining cis-Golgi structure. {ECO:0000269|PubMed:10189370, ECO:0000269|PubMed:9256431}.; ","gedi|level2",{"$nulls":3},"p.Arg1814Met","c.5441G>T","MODERATE","1814/1979",18,{"$nulls":5},"5","610","656","406","450","510","552","0","0","0","0.0996",{"$nulls":20},"3.277805","3.65","1.935","0.99999","-2.94","0.996","0.003","0.427",{"$nulls":3},"ExAC_AFR_AF",9.61e-05,"AR","Achondrogenesis, type IA","Musculoskeletal","COSMIC",null,null,"C0265273| C2745953","0/0","588,0","0","588","0/1","565,60","0.096","625",null,"chr14:91975188:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0978"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TRPM6","chr9:74786017","TRPM6(V926I)",null,null,"transmembrane region (Helical ), splice variant (In isoform M6-kinase 3. ), splice variant (In isoform M6-kinase 2. ), splice variant (In isoform M6-kinase 1. )",{"$nulls":3},255,"PASS","Missense","rs140835112",0.003632589517384536,null,"FUNCTION: Essential ion channel and serine/threonine-protein kinase. Crucial for magnesium homeostasis. Has an important role in epithelial magnesium transport and in the active magnesium absorption in the gut and kidney. Isoforms of the type M6-kinase lack the ion channel region.; ",{"$nulls":4},"p.Val926Ile","c.2776G>A","MODERATE","926/2022",21,1,{"$nulls":4},"5","402","406","292","291","345","343","0","0","0","0.0991",{"$nulls":20},"0.908396","-0.86",".;.;0.625","1;1;1;1;1;1;0.999869;0.999869","-0.38","0.035;.;0.74","1.0","0.035;0.033;0.037",{"$nulls":3},"ALSPAC_AF",0.003632589517384536,"AR","Hypomagnesemia 1, intestinal","Gastrointestinal",{"$nulls":3},"C1865974","0/0","386,0","0","386","0/1","351,41","0.1046","392",null,"chr9:74786017:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.11"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TRPM6","chr9:74786017","TRPM6(V926I)",null,null,"transmembrane region (Helical ), splice variant (In isoform M6-kinase 3. ), splice variant (In isoform M6-kinase 2. ), splice variant (In isoform M6-kinase 1. )",{"$nulls":3},255,"PASS","Missense","rs140835112",0.003632589517384536,null,"FUNCTION: Essential ion channel and serine/threonine-protein kinase. Crucial for magnesium homeostasis. Has an important role in epithelial magnesium transport and in the active magnesium absorption in the gut and kidney. Isoforms of the type M6-kinase lack the ion channel region.; ",{"$nulls":4},"p.Val926Ile","c.2776G>A","MODERATE","926/2022",21,1,{"$nulls":4},"4","402","434","292","304","346","360","0","0","0","0.0583",{"$nulls":20},"0.908396","-0.86",".;.;0.625","1;1;1;1;1;1;0.999869;0.999869","-0.38","0.035;.;0.74","1.0","0.035;0.033;0.037",{"$nulls":3},"ALSPAC_AF",0.003632589517384536,"AR","Hypomagnesemia 1, intestinal","Gastrointestinal",{"$nulls":3},"C1865974","0/0","382,0","0","382","0/1","390,22","0.0534","412",null,"chr9:74786017:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0592"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TTC28","chr22:28105557","TTC28(L1003fs)",null,null,"repeat (TPR 24 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: During mitosis, may be involved in the condensation of spindle midzone microtubules, leading to the formation of midbody. {ECO:0000269|PubMed:23036704}.; ",{"$nulls":4},"p.Leu1003fs","c.3007_3028delCTGGGGGGCGTTTACCAGCAGA","HIGH","1003/2481",8,{"$nulls":5},"4","477","540","369","463","405","485","0","0","0","0.3278",{"$nulls":5},"(TTC28|ENSG00000100154|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","552,0","0","552","0/1","437,186","0.2986","623",null,"chr22:28105557:ATCTGCTGGTAAACGCCCCCCAG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3542"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TTC28","chr22:28105557","TTC28(L1003fs)",null,null,"repeat (TPR 24 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: During mitosis, may be involved in the condensation of spindle midzone microtubules, leading to the formation of midbody. {ECO:0000269|PubMed:23036704}.; ",{"$nulls":4},"p.Leu1003fs","c.3007_3028delCTGGGGGGCGTTTACCAGCAGA","HIGH","1003/2481",8,{"$nulls":5},"4","477","520","369","389","406","432","0","0","0","0.1829",{"$nulls":5},"(TTC28|ENSG00000100154|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","553,0","0","553","0/1","503,85","0.1446","588",null,"chr22:28105557:ATCTGCTGGTAAACGCCCCCCAG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1568"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TTLL12","chr22:43186896","TTLL12(H58Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.His58Gln","c.174C>G","MODERATE","58/644",1,{"$nulls":5},"5","115","117","91","93","83","81","0","0","0","0.0741",{"$nulls":20},"2.44436","3.33","2.395","0.715925","-1.25","0.664","0.442","0.24",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","112,0","0","112","0/1","105,7","0.0625","112",null,"chr22:43186896:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0753"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TTN","chr2:178612403","TTN(T16708S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Thr16708Ser","c.50122A>T","MODERATE","16708/35991",266,{"$nulls":5},"4","1914","2820","1437","2139","1438","2128","0.0005","0.0005","0","0.1358",{"$nulls":20},"2.931334","0.34;0.34;0.34;0.34;0.34;0.34;.",".;.;.;2.195;.;.;2.195","0.984244","-2.49;-2.53;.;.;-2.53;-2.53;.",".;.;.;0.891;.;.;0.891","0.171;0.06;.;.;0.09;0.078;.","0.439;0.462;0.367;0.356;0.462;0.462;0.355",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","1691,1","0.0006","1692","0/1","2140,346","0.1392","2486",null,"chr2:178612403:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1346"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","TTN","chr2:178612403","TTN(T16708S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Thr16708Ser","c.50122A>T","MODERATE","16708/35991",266,{"$nulls":5},"4","1914","2597","1437","1978","1440","1968","0.0005","0.0005","0","0.062",{"$nulls":20},"2.931334","0.34;0.34;0.34;0.34;0.34;0.34;.",".;.;.;2.195;.;.;2.195","0.984244","-2.49;-2.53;.;.;-2.53;-2.53;.",".;.;.;0.891;.;.;0.891","0.171;0.06;.;.;0.09;0.078;.","0.439;0.462;0.367;0.356;0.462;0.462;0.355",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","1684,1","0.0006","1685","0/1","2167,149","0.0643","2316",null,"chr2:178612403:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0688"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","TUBA3E","chr2:130194139","TUBA3E(V235M)",{"$nulls":6},255,"PASS","Missense","rs772701111",1.499E-5,null,"FUNCTION: Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Val235Met","c.703G>A","MODERATE","235/450",4,1,{"$nulls":4},"3",null,null,"866","1109","1083","401",null,null,"0","0.0798",{"$nulls":20},"3.3225350000000002","-0.38","0.32","0.999335","-1.89","1.0",null,"0.68",{"$nulls":3},"ExAC_NFE_AF",1.499E-5,{"$nulls":7},"0/0","1079,0","0","1079","0/1","1199,140","0.1046","1339",null,"chr2:130194139:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1019"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","UBQLN4","chr1:156051791","UBQLN4(F56_G58del)",null,null,"domain (Ubiquitin-like )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Plays a role in the regulation of protein degradation via the ubiquitin-proteasome system (UPS). Mediates the proteasomal targeting of misfolded or accumulated proteins for degradation by binding (via UBA domain) to their polyubiquitin chains and by interacting (via ubiquitin-like domain) with the subunits of the proteasome (Ref. 6). Plays a role in the regulation of the proteasomal degradation of non-ubiquitinated GJA1 (By similarity). Acts as an adapter protein that recruits UBQLN1 to the autophagy machinery. Mediates the association of UBQLN1 with autophagosomes and the autophagy-related protein LC3 (MAP1LC3A/B/C) and may assist in the maturation of autophagosomes to autolysosomes by mediating autophagosome-lysosome fusion (PubMed:23459205). {ECO:0000250|UniProtKB:Q99NB8, ECO:0000269|PubMed:15280365, ECO:0000269|PubMed:23459205}.; ",{"$nulls":4},"p.Phe56_Gly58del","c.166_174delTTCGCAGGC","MODERATE","56/601",2,{"$nulls":5},"4","758","785","557","596","681","672","0","0","0","0.0521",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","772,0","0","772","0/1","688,96","0.1224","784",null,"chr1:156051791:TGCCTGCGAA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1258"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","UBR1","chr15:43068026","UBR1(E224*)",{"$nulls":6},54,"PASS","Loss Of Function",null,-1,"DISEASE: Johanson-Blizzard syndrome (JBS) [MIM:243800]: This disorder includes congenital exocrine pancreatic insufficiency, multiple malformations such as nasal wing aplasia, and frequent mental retardation. Pancreas of individuals with JBS do not express UBR1 and show intrauterine-onset destructive pancreatitis. {ECO:0000269|PubMed:16311597, ECO:0000269|PubMed:21931868, ECO:0000269|PubMed:22072859, ECO:0000269|PubMed:24599544, ECO:0000269|PubMed:26149651}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. May be involved in pancreatic homeostasis. Binds leucine and is a negative regulator of the leucine-mTOR signaling pathway, thereby controlling cell growth. {ECO:0000269|PubMed:15548684, ECO:0000269|PubMed:16311597, ECO:0000269|PubMed:20298436, ECO:0000269|PubMed:20835242}.; ",{"$nulls":4},"p.Glu224*","c.670G>T","HIGH","224/1749",6,{"$nulls":5},"1",{"$nulls":15},"(UBR1|ENSG00000159459|1|1.00)","(UBR1|ENSG00000159459|1|1.00)",{"$nulls":13},"6.7059560000000005",null,null,"1",{"$nulls":3},"0.88;0.868",{"$nulls":3},"Unknown",-1,"AR","Johanson-Blizzard syndrome","Audiologic/Otolaryngologic; Craniofacial; Dental; Dermatologic; Cardiovascular; Endocrine; Gastrointestinal; Hematologic; Neurologic; Ophthalmologic",{"$nulls":3},"C0175692","0/0","85,0","0","85","0/1","90,5","0.0526","95",null,"chr15:43068026:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0526"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","UBR3","chr2:169949855","UBR3(L1112R)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end rule pathway (By similarity). Does not bind to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation (By similarity). May play a role in Shh signaling by mediating the ubiquitination of Kif7 (By similarity). May be important for MYH9 function in certain tissues, possibly by regulating the ubiquitination of MYH9 and consequently affecting its interaction with MYO7A (PubMed:27331610). {ECO:0000250|UniProtKB:Q5U430, ECO:0000269|PubMed:27331610}.; ",{"$nulls":4},"p.Leu1112Arg","c.3335T>G","MODERATE","1112/1888",23,{"$nulls":5},"5","297","314","209","228","269","271","0","0","0","0.1255",{"$nulls":20},"3.333613","0.49","0.975","0.697612","-2.18","0.997","0.007","0.718;0.667",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","278,0","0","278","0/1","271,35","0.1144","306",null,"chr2:169949855:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1053"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","UNC5CL","chr6:41028564","UNC5CL(A456T)",null,null,"topological domain (Cytoplasmic ), domain (Death )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibits NF-kappa-B-dependent transcription by impairing NF-kappa-B binding to its targets. {ECO:0000269|PubMed:14769797}.; ",{"$nulls":4},"p.Ala456Thr","c.1366G>A","MODERATE","456/518",9,{"$nulls":5},"5","654","621","460","447","609","566","0","0","0","0.182",{"$nulls":20},"2.536648","-2.07","1.245","0.806137","-0.26","0.473","0.386","0.44;0.552",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","645,0","0","645","0/1","492,116","0.1908","608",null,"chr6:41028564:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1812"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","UNC5CL","chr6:41028564","UNC5CL(A456T)",null,null,"topological domain (Cytoplasmic ), domain (Death )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibits NF-kappa-B-dependent transcription by impairing NF-kappa-B binding to its targets. {ECO:0000269|PubMed:14769797}.; ",{"$nulls":4},"p.Ala456Thr","c.1366G>A","MODERATE","456/518",9,{"$nulls":5},"5","654","696","460","493","610","620","0","0","0","0.0806",{"$nulls":20},"2.536648","-2.07","1.245","0.806137","-0.26","0.473","0.386","0.44;0.552",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","645,0","0","645","0/1","619,61","0.0897","680",null,"chr6:41028564:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0811"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","USH2A","chr1:215640673","USH2A(W4951C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269|PubMed:10729113, ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:11311042, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12525556, ECO:0000269|PubMed:14970843, ECO:0000269|PubMed:15015129, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17405132, ECO:0000269|PubMed:18273898, ECO:0000269|PubMed:18452394, ECO:0000269|PubMed:19683999, ECO:0000269|PubMed:19737284, ECO:0000269|PubMed:20309401, ECO:0000269|PubMed:20440071, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21593743, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22004887, ECO:0000269|PubMed:23737954, ECO:0000269|PubMed:26377068, ECO:0000269|PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in USH2A has been found in a patient with a form of non-syndromic sensorineural hearing loss. {ECO:0000269|PubMed:25388789}.; ","FUNCTION: Involved in hearing and vision.; ",{"$nulls":4},"p.Trp4951Cys","c.14853G>C","MODERATE","4951/5202",68,{"$nulls":5},"5","465","608","309","397","432","572","0","0","0","0.1031",{"$nulls":20},"3.660261","0.82","2.455","1","-9.36","1.0",null,"0.881",{"$nulls":3},"Unknown",-1,"AR","Usher syndrome, type 2A","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008].",null,"C3151138| C1848634","0/0","448,0","0","448","0/1","528,66","0.1111","594",null,"chr1:215640673:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1159"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","USH2A","chr1:216097184","USH2A(P1553S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269|PubMed:10729113, ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:11311042, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12525556, ECO:0000269|PubMed:14970843, ECO:0000269|PubMed:15015129, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17405132, ECO:0000269|PubMed:18273898, ECO:0000269|PubMed:18452394, ECO:0000269|PubMed:19683999, ECO:0000269|PubMed:19737284, ECO:0000269|PubMed:20309401, ECO:0000269|PubMed:20440071, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21593743, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22004887, ECO:0000269|PubMed:23737954, ECO:0000269|PubMed:26377068, ECO:0000269|PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in USH2A has been found in a patient with a form of non-syndromic sensorineural hearing loss. {ECO:0000269|PubMed:25388789}.; ","FUNCTION: Involved in hearing and vision.; ",{"$nulls":4},"p.Pro1553Ser","c.4657C>T","MODERATE","1553/5202",22,{"$nulls":5},"5","205","281","129","176","183","247","0","0","0","0.17",{"$nulls":20},"2.396162","-1.18","0.73","0.708515","-3.61","0.751","0.154","0.279",{"$nulls":3},"Unknown",-1,"AR","Usher syndrome, type 2A","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008].",null,"C3151138| C1848634","0/0","194,0","0","194","0/1","223,47","0.1741","270",null,"chr1:216097184:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1648"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","USH2A","chr1:216097184","USH2A(P1553S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269|PubMed:10729113, ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:11311042, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12525556, ECO:0000269|PubMed:14970843, ECO:0000269|PubMed:15015129, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17405132, ECO:0000269|PubMed:18273898, ECO:0000269|PubMed:18452394, ECO:0000269|PubMed:19683999, ECO:0000269|PubMed:19737284, ECO:0000269|PubMed:20309401, ECO:0000269|PubMed:20440071, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21593743, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22004887, ECO:0000269|PubMed:23737954, ECO:0000269|PubMed:26377068, ECO:0000269|PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in USH2A has been found in a patient with a form of non-syndromic sensorineural hearing loss. {ECO:0000269|PubMed:25388789}.; ","FUNCTION: Involved in hearing and vision.; ",{"$nulls":4},"p.Pro1553Ser","c.4657C>T","MODERATE","1553/5202",22,{"$nulls":5},"4","205","266","129","171",null,null,"0","0",{"$nulls":22},"2.396162","-1.18","0.73","0.708515","-3.61","0.751","0.154","0.279",{"$nulls":3},"Unknown",-1,"AR","Usher syndrome, type 2A","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008].",null,"C3151138| C1848634","0/0","185,0","0","185","0/1","227,15","0.062","242",null,"chr1:216097184:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0585"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","USP12","chr13:27116569","USP12(E26Q)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Deubiquitinating enzyme. Has almost no deubiquitinating activity by itself and requires the interaction with WDR20 and WDR48 to have a high activity (PubMed:19075014, PubMed:27373336). Not involved in deubiquitination of monoubiquitinated FANCD2 (PubMed:19075014). In complex with WDR48, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). {ECO:0000269|PubMed:19075014, ECO:0000269|PubMed:24145035, ECO:0000269|PubMed:27373336}.; ",{"$nulls":4},"p.Glu26Gln","c.76G>C","MODERATE","26/370",2,{"$nulls":5},"5","114","136","94","108","90","116","0","0","0","0.1121",{"$nulls":20},"3.017036","1.9","0.805","1","-1.26","0.825","0.087","0.619",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","113,0","0","113","0/1","115,16","0.1221","131",null,"chr13:27116569:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1019"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","USP12","chr13:27116569","USP12(E26Q)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Deubiquitinating enzyme. Has almost no deubiquitinating activity by itself and requires the interaction with WDR20 and WDR48 to have a high activity (PubMed:19075014, PubMed:27373336). Not involved in deubiquitination of monoubiquitinated FANCD2 (PubMed:19075014). In complex with WDR48, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). {ECO:0000269|PubMed:19075014, ECO:0000269|PubMed:24145035, ECO:0000269|PubMed:27373336}.; ",{"$nulls":4},"p.Glu26Gln","c.76G>C","MODERATE","26/370",2,{"$nulls":5},"5","114","132","94","110","90","85","0","0","0","0.0824",{"$nulls":20},"3.017036","1.9","0.805","1","-1.26","0.825","0.087","0.619",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","112,0","0","112","0/1","122,10","0.0758","132",null,"chr13:27116569:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0818"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","USP17L17","chr4:9244799","USP17L17(M307I)",{"$nulls":6},74,"PASS","Missense",null,-1,null,"FUNCTION: Deubiquitinating enzyme that removes conjugated ubiquitin from specific proteins to regulate different cellular processes that may include cell proliferation, progression through the cell cycle, apoptosis, cell migration, and the cellular response to viral infection. {ECO:0000250}.; ",{"$nulls":4},"p.Met307Ile","c.921G>T","MODERATE","307/558",1,{"$nulls":5},"1",{"$nulls":30},"1.6248399999999998","1.61;.","1.19;.","0.978539","-2.46;.",null,"0.053;.","0.187;0.182",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","124,0","0","124","0/1","66,4","0.0563","71",null,"chr4:9244799:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0563"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","USP24","chr1:55110194","USP24(D1521N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Ubiquitin-specific protease that regulates cell survival in various contexts through modulating the protein stability of some of its substrates including DDB2, MCL1 or TP53. Plays a positive role on ferritinophagy where ferritin is degraded in lysosomes and releases free iron. {ECO:0000269|PubMed:23159851, ECO:0000269|PubMed:29695420}.; ",{"$nulls":4},"p.Asp1521Asn","c.4561G>A","MODERATE","1521/2620",39,{"$nulls":5},"2",null,null,"64","71",{"$nulls":26},"2.971334","-0.23","1.61","1","-1.2",null,"1.0","0.595",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","79,0","0","79","0/1","85,7","0.0761","92",null,"chr1:55110194:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0845"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","USP24","chr1:55110194","USP24(D1521N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Ubiquitin-specific protease that regulates cell survival in various contexts through modulating the protein stability of some of its substrates including DDB2, MCL1 or TP53. Plays a positive role on ferritinophagy where ferritin is degraded in lysosomes and releases free iron. {ECO:0000269|PubMed:23159851, ECO:0000269|PubMed:29695420}.; ",{"$nulls":4},"p.Asp1521Asn","c.4561G>A","MODERATE","1521/2620",39,{"$nulls":5},"4","79","101","64","79","56","85","0","0","0","0.1059",{"$nulls":20},"2.971334","-0.23","1.61","1","-1.2",null,"1.0","0.595",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","77,0","0","77","0/1","91,10","0.099","101",null,"chr1:55110194:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1139"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","VCPIP1","chr8:66665472","VCPIP1(K496R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a deubiquitinating enzyme. Necessary for VCP- mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER). Mediates dissociation of the ternary complex containing STX5A, NSFL1C and VCP (By similarity). Hydrolyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitin chains. {ECO:0000250, ECO:0000269|PubMed:23827681}.; ",{"$nulls":4},"p.Lys496Arg","c.1487A>G","MODERATE","496/1222",1,{"$nulls":5},"4","440","784","342","604","402","674","0","0","0","0.3769",{"$nulls":20},"2.368649","1.44","2.08","0.999433","-0.47","0.006","0.472","0.349",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","436,0","0","436","0/1","457,296","0.3931","753",null,"chr8:66665472:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3791"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","VCPIP1","chr8:66665472","VCPIP1(K496R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a deubiquitinating enzyme. Necessary for VCP- mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER). Mediates dissociation of the ternary complex containing STX5A, NSFL1C and VCP (By similarity). Hydrolyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitin chains. {ECO:0000250, ECO:0000269|PubMed:23827681}.; ",{"$nulls":4},"p.Lys496Arg","c.1487A>G","MODERATE","496/1222",1,{"$nulls":5},"5","440","737","342","574","402","627","0","0","0","0.252",{"$nulls":20},"2.368649","1.44","2.08","0.999433","-0.47","0.006","0.472","0.349",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","437,0","0","437","0/1","536,183","0.2545","719",null,"chr8:66665472:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2578"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","VWA3B","chr2:98312326","VWA3B(R1288W)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia, autosomal recessive, 22 (SCAR22) [MIM:616948]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR22 patients manifest variable severity of intellectual disability associated with adult-onset cerebellar ataxia. {ECO:0000269|PubMed:26157035}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ",{"$nulls":5},"p.Arg1288Trp","c.3862A>T","MODERATE","1288/1294",28,{"$nulls":5},"5","262","311","176","213","246","287","0","0","0","0.1603",{"$nulls":20},"2.262209","3.18;.","1.24;.","1","-2.51;.","0.003;.","0.016;.","0.129;0.243",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310781","0/0","246,0","0","246","0/1","240,51","0.1753","291",null,"chr2:98312326:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1831"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","VWC2","chr7:49775756","VWC2(D108fs)",{"$nulls":3},"short-sequence-motif:Mediates_cell_adhesion, compositionally-biased-region:Poly-Ala","LOW, LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: BMP antagonist which may play a role in neural development. Promotes cell adhesion (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp108fs","c.323_360delATCTGCAGGTCCGGCCCCGCGGGGACACCCCGCAGGCG","HIGH","108/325",2,{"$nulls":5},"4","365","586","326","524","215","486","0.0111","0.0111","0","0.4198",{"$nulls":5},"(VWC2|ENSG00000188730|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","543,0","0","543","0/1","578,159","0.2157","737",null,"chr7:49775756:GGATCTGCAGGTCCGGCCCCGCGGGGACACCCCGCAGGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3531"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","VWC2","chr7:49775756","VWC2(D108fs)",{"$nulls":3},"short-sequence-motif:Mediates_cell_adhesion, compositionally-biased-region:Poly-Ala","LOW, LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: BMP antagonist which may play a role in neural development. Promotes cell adhesion (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp108fs","c.323_360delATCTGCAGGTCCGGCCCCGCGGGGACACCCCGCAGGCG","HIGH","108/325",2,{"$nulls":5},"4",null,null,"326","411","215","319",null,null,"0","0.1191",{"$nulls":5},"(VWC2|ENSG00000188730|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","544,0","0","544","0/1","627,41","0.0614","668",null,"chr7:49775756:GGATCTGCAGGTCCGGCCCCGCGGGGACACCCCGCAGGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0973"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WAC","chr10:28595856","WAC(P245L)",null,null,"splice variant (In isoform 4. ), sequence variant (Probable disease-associated variant found in a patient severe intellectual disability. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: DeSanto-Shinawi syndrome (DESSH) [MIM:616708]: An autosomal dominant syndrome characterized by developmental delay, hypotonia, behavioral problems, eye abnormalities, constipation, feeding difficulties, seizures and sleep problems. Patients exhibit dysmorphic features, including broad/prominent forehead, synophrys and/or bushy eyebrows, depressed nasal bridge and bulbous nasal tip. Additional variable features are posteriorly rotated ears, hirsutism, deep-set eyes, thin upper lip, inverted nipples, hearing loss and branchial cleft anomalies. {ECO:0000269|PubMed:25356899, ECO:0000269|PubMed:26264232}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in WAC are the cause of a form of intellectual disability characterized by hypotonia, behavioral problems and distinctive facial dysmorphisms including a square- shaped face, deep set eyes, long palpebral fissures, and a broad mouth and chin. {ECO:0000269|PubMed:26757981}.; ","FUNCTION: Acts as a linker between gene transcription and histone H2B monoubiquitination at 'Lys-120' (H2BK120ub1) (PubMed:21329877). Interacts with the RNA polymerase II transcriptional machinery via its WW domain and with RNF20-RNF40 via its coiled coil region, thereby linking and regulating H2BK120ub1 and gene transcription (PubMed:21329877). Regulates the cell-cycle checkpoint activation in response to DNA damage (PubMed:21329877). Positive regulator of amino acid starvation- induced autophagy (PubMed:22354037). Also acts as a negative regulator of basal autophagy (PubMed:26812014). Positively regulates MTOR activity by promoting, in an energy-dependent manner, the assembly of the TTT complex composed of TELO2, TTI1 and TTI2 and the RUVBL complex composed of RUVBL1 and RUVBL2 into the TTT-RUVBL complex. This leads to the dimerization of the mTORC1 complex and its subsequent activation (PubMed:26812014). May negatively regulate the ubiquitin proteasome pathway (PubMed:21329877). {ECO:0000269|PubMed:21329877, ECO:0000269|PubMed:22354037, ECO:0000269|PubMed:26812014}.; ",{"$nulls":4},"p.Pro245Leu","c.734C>T","MODERATE","245/647",7,{"$nulls":5},"5","491","523","375","405","394","426","0","0","0","0.3991",{"$nulls":20},"3.516466","2.01;2.0;0.71;1.0",".;1.245;.;.","1","-1.88;-1.88;-4.26;-2.94","0.999;0.998;.;.","0.002;.;0.0;0.0","0.486;0.548;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225239","0/0","465,0","0","465","0/1","307,198","0.3921","505",null,"chr10:28595856:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3951"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","WAC","chr10:28595856","WAC(P245L)",null,null,"splice variant (In isoform 4. ), sequence variant (Probable disease-associated variant found in a patient severe intellectual disability. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: DeSanto-Shinawi syndrome (DESSH) [MIM:616708]: An autosomal dominant syndrome characterized by developmental delay, hypotonia, behavioral problems, eye abnormalities, constipation, feeding difficulties, seizures and sleep problems. Patients exhibit dysmorphic features, including broad/prominent forehead, synophrys and/or bushy eyebrows, depressed nasal bridge and bulbous nasal tip. Additional variable features are posteriorly rotated ears, hirsutism, deep-set eyes, thin upper lip, inverted nipples, hearing loss and branchial cleft anomalies. {ECO:0000269|PubMed:25356899, ECO:0000269|PubMed:26264232}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in WAC are the cause of a form of intellectual disability characterized by hypotonia, behavioral problems and distinctive facial dysmorphisms including a square- shaped face, deep set eyes, long palpebral fissures, and a broad mouth and chin. {ECO:0000269|PubMed:26757981}.; ","FUNCTION: Acts as a linker between gene transcription and histone H2B monoubiquitination at 'Lys-120' (H2BK120ub1) (PubMed:21329877). Interacts with the RNA polymerase II transcriptional machinery via its WW domain and with RNF20-RNF40 via its coiled coil region, thereby linking and regulating H2BK120ub1 and gene transcription (PubMed:21329877). Regulates the cell-cycle checkpoint activation in response to DNA damage (PubMed:21329877). Positive regulator of amino acid starvation- induced autophagy (PubMed:22354037). Also acts as a negative regulator of basal autophagy (PubMed:26812014). Positively regulates MTOR activity by promoting, in an energy-dependent manner, the assembly of the TTT complex composed of TELO2, TTI1 and TTI2 and the RUVBL complex composed of RUVBL1 and RUVBL2 into the TTT-RUVBL complex. This leads to the dimerization of the mTORC1 complex and its subsequent activation (PubMed:26812014). May negatively regulate the ubiquitin proteasome pathway (PubMed:21329877). {ECO:0000269|PubMed:21329877, ECO:0000269|PubMed:22354037, ECO:0000269|PubMed:26812014}.; ",{"$nulls":4},"p.Pro245Leu","c.734C>T","MODERATE","245/647",7,{"$nulls":5},"5","491","571","375","438","395","454","0","0","0","0.2093",{"$nulls":20},"3.516466","2.01;2.0;0.71;1.0",".;1.245;.;.","1","-1.88;-1.88;-4.26;-2.94","0.999;0.998;.;.","0.002;.;0.0;0.0","0.486;0.548;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225239","0/0","464,0","0","464","0/1","442,109","0.1978","551",null,"chr10:28595856:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2078"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WDR1","chr4:10103916","WDR1(G70A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Induces disassembly of actin filaments in conjunction with ADF/cofilin family proteins (PubMed:15629458). Enhances cofilin-mediated actin severing (By similarity). Involved in cytokinesis. Involved in chemotactic cell migration by restricting lamellipodial membrane protrusions (PubMed:18494608). Involved in myocardium sarcomere organization. Required for cardiomyocyte growth and maintenance (By similarity). Involved in megakaryocyte maturation and platelet shedding. Required for the establishment of planar cell polarity (PCP) during follicular epithelium development and for cell shape changes during PCP; the function seems to implicate cooperation with CFL1 and/or DSTN/ADF. Involved in the generation/maintenance of cortical tension (By similarity). Involved in assembly and maintenance of epithelial apical cell junctions and plays a role in the organization of the perijunctional actomyosin belt (PubMed:25792565). {ECO:0000250|UniProtKB:O88342, ECO:0000250|UniProtKB:Q9W7F2, ECO:0000269|PubMed:15629458, ECO:0000269|PubMed:18494608, ECO:0000269|PubMed:25792565}.; ",{"$nulls":4},"p.Gly70Ala","c.209G>C","MODERATE","70/606",3,{"$nulls":5},"5","412","497","292","370","343","401","0","0","0","0.1197",{"$nulls":20},"3.889475","-0.18;-0.18;0.08","3.43;3.43;.","1","-5.47;-5.47;-5.82","1.0;1.0;.","0.0;0.0;0.027","0.906;0.905;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","396,0","0","396","0/1","420,62","0.1286","482",null,"chr4:10103916:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1243"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","WDR1","chr4:10103916","WDR1(G70A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Induces disassembly of actin filaments in conjunction with ADF/cofilin family proteins (PubMed:15629458). Enhances cofilin-mediated actin severing (By similarity). Involved in cytokinesis. Involved in chemotactic cell migration by restricting lamellipodial membrane protrusions (PubMed:18494608). Involved in myocardium sarcomere organization. Required for cardiomyocyte growth and maintenance (By similarity). Involved in megakaryocyte maturation and platelet shedding. Required for the establishment of planar cell polarity (PCP) during follicular epithelium development and for cell shape changes during PCP; the function seems to implicate cooperation with CFL1 and/or DSTN/ADF. Involved in the generation/maintenance of cortical tension (By similarity). Involved in assembly and maintenance of epithelial apical cell junctions and plays a role in the organization of the perijunctional actomyosin belt (PubMed:25792565). {ECO:0000250|UniProtKB:O88342, ECO:0000250|UniProtKB:Q9W7F2, ECO:0000269|PubMed:15629458, ECO:0000269|PubMed:18494608, ECO:0000269|PubMed:25792565}.; ",{"$nulls":4},"p.Gly70Ala","c.209G>C","MODERATE","70/606",3,{"$nulls":5},"4",null,null,"292","384","343","439",null,null,"0","0.0524",{"$nulls":20},"3.889475","-0.18;-0.18;0.08","3.43;3.43;.","1","-5.47;-5.47;-5.82","1.0;1.0;.","0.0;0.0;0.027","0.906;0.905;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","396,0","0","396","0/1","478,26","0.0516","504",null,"chr4:10103916:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0573"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WDR17","chr4:176125290","WDR17(S266T)",{"$nulls":3},"repeat:WD_5","LOW",null,255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser266Thr","c.797G>C","MODERATE","266/1322",6,{"$nulls":5},"5","246","239","178","171","224","212","0","0","0","0.1745",{"$nulls":20},"1.7031960000000002","-0.16;-0.16;.",".;0.81;.","0.998463","-1.28",".;0.001;.","0.277;0.258;0.262","0.113;0.13;0.218",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","245,0","0","245","0/1","192,39","0.1688","231",null,"chr4:176125290:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1696"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","WDR17","chr4:176125290","WDR17(S266T)",{"$nulls":3},"repeat:WD_5","LOW",null,255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser266Thr","c.797G>C","MODERATE","266/1322",6,{"$nulls":5},"5","246","226","178","161","225","200","0","0","0","0.08",{"$nulls":20},"1.7031960000000002","-0.16;-0.16;.",".;0.81;.","0.998463","-1.28",".;0.001;.","0.277;0.258;0.262","0.113;0.13;0.218",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","241,0","0","241","0/1","206,20","0.0885","226",null,"chr4:176125290:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0994"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WDR48","chr3:39088156","WDR48(Q501H)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 and USP46 (PubMed:18082604, PubMed:19075014, PubMed:26388029). Enhances the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself (PubMed:18082604). Also activates deubiquitinating activity of complexes containing USP12 (PubMed:19075014, PubMed:27650958, PubMed:27373336). Docks at the distal end of the USP12 fingers domain and induces a cascade of structural changes leading to the activation of the enzyme (PubMed:27650958, PubMed:27373336). Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate (PubMed:19075014, PubMed:27373336). In complex with USP12, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). In case of infection by Herpesvirus saimiri, may play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes. Induces lysosomal vesicle formation via interaction with Herpesvirus saimiri tyrosine kinase-interacting protein (TIP). Subsequently, TIP recruits tyrosine-protein kinase LCK, resulting in down-regulation of T-cell antigen receptor TCR. May play a role in generation of enlarged endosomal vesicles via interaction with TIP (PubMed:12196293). In case of infection by papillomavirus HPV11, promotes the maintenance of the viral genome via its interaction with HPV11 helicase E1 (PubMed:18032488). {ECO:0000269|PubMed:12196293, ECO:0000269|PubMed:18032488, ECO:0000269|PubMed:18082604, ECO:0000269|PubMed:19075014, ECO:0000269|PubMed:24145035, ECO:0000269|PubMed:26388029, ECO:0000269|PubMed:27373336, ECO:0000269|PubMed:27650958}.; ",{"$nulls":4},"p.Gln501His","c.1503G>C","MODERATE","501/677",15,{"$nulls":5},"5","380","391","264","276","339","342","0","0","0","0.1754",{"$nulls":20},"2.468575","1.17","1.24","1","-0.35","0.577","0.512","0.609",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","347,0","0","347","0/1","309,64","0.1716","373",null,"chr3:39088156:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1667"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WDR64","chr1:241772816","WDR64(G762A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly762Ala","c.2285G>C","MODERATE","762/1081",19,{"$nulls":5},"5","290","366","222","279","213","286","0","0","0","0.1014",{"$nulls":20},"0.096388","1.18","1.87","1","-0.64","0.049","0.167","0.105",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","281,0","0","281","0/1","323,34","0.0952","357",null,"chr1:241772816:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1039"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","WDR64","chr1:241772816","WDR64(G762A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly762Ala","c.2285G>C","MODERATE","762/1081",19,{"$nulls":5},"4","290","355",null,null,"214","253","0","0","0","0.0593",{"$nulls":20},"0.096388","1.18","1.87","1","-0.64","0.049","0.167","0.105",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","281,0","0","281","0/1","325,20","0.058","345",null,"chr1:241772816:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WDR78","chr1:66814181","WDR78(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.2497-1G>C","HIGH",null,16,{"$nulls":5},"5","118","112","74","69","104","98","0","0","0","0.1327",{"$nulls":5},"(WDR78|ENSG00000152763|1|1.00)",{"$nulls":14},"4.054045",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","112,0","0","112","0/1","93,16","0.1468","109",null,"chr1:66814181:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1739"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","WWP2","chr16:69798690","WWP2(A27P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Polyubiquitinates POU5F1 by 'Lys-63'-linked conjugation and promotes it to proteasomal degradation; in embryonic stem cells (ESCs) the ubiquitination is proposed to regulate POU5F1 protein level. Ubiquitinates EGR2 and promotes it to proteasomal degradation; in T-cells the ubiquitination inhibits activation- induced cell death. Ubiquitinates SLC11A2; the ubiquitination is enhanced by presence of NDFIP1 and NDFIP2. Ubiquitinates RPB1 and promotes it to proteasomal degradation. {ECO:0000269|PubMed:19274063, ECO:0000269|PubMed:19651900}.; ",{"$nulls":4},"p.Ala27Pro","c.79G>C","MODERATE","27/870",3,{"$nulls":5},"5","231","164","185","132","187","136","0","0","0","0.1985",{"$nulls":20},"4.164483","-1.44;-1.44;.;-1.44","2.07;.;.;2.07","1","-2.84;-4.52;-4.67;-3.68","0.985;.;.;.","0.001;0.002;0.009;0.003","0.863;.;.;0.667",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","225,0","0","225","0/1","131,30","0.1863","161",null,"chr16:69798690:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1742"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","XPNPEP2","chrX:129754564","XPNPEP2(I400M)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Angioedema induced by ACE inhibitors (AEACEI) [MIM:300909]: A potentially life-threatening side effect of ACE inhibitors that appears in a subset of patients taking these drugs for hypertension and cardiovascular disease treatment. AEACEI is characterized by swelling of the face, lips, tongue, and airway that can lead to suffocation and death if severe. {ECO:0000269|PubMed:16175507, ECO:0000269|PubMed:20625347, ECO:0000269|PubMed:21898657}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Membrane-bound metalloprotease which catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides, such as Arg-Pro-Pro. May play a role in the metabolism of the vasodilator bradykinin. {ECO:0000269|PubMed:15361070}.; ",{"$nulls":4},"p.Ile400Met","c.1200C>G","MODERATE","400/674",12,{"$nulls":5},"5","691","736","482","510","610","641","0","0","0","0.1357",{"$nulls":20},"0.117028","-0.99","-0.025","1","1.1","0.069","0.172","0.12",{"$nulls":3},"Unknown",-1,"XL","Angioedema induced by ACE inhibitors, susceptibility to","General",{"$nulls":3},"C3806711","0/0","666,0","0","666","0/1","607,99","0.1402","706",null,"chrX:129754564:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1392"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","XPNPEP2","chrX:129754564","XPNPEP2(I400M)",{"$nulls":6},100.778,"PASS","Missense",null,-1,"DISEASE: Angioedema induced by ACE inhibitors (AEACEI) [MIM:300909]: A potentially life-threatening side effect of ACE inhibitors that appears in a subset of patients taking these drugs for hypertension and cardiovascular disease treatment. AEACEI is characterized by swelling of the face, lips, tongue, and airway that can lead to suffocation and death if severe. {ECO:0000269|PubMed:16175507, ECO:0000269|PubMed:20625347, ECO:0000269|PubMed:21898657}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Membrane-bound metalloprotease which catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides, such as Arg-Pro-Pro. May play a role in the metabolism of the vasodilator bradykinin. {ECO:0000269|PubMed:15361070}.; ",{"$nulls":4},"p.Ile400Met","c.1200C>G","MODERATE","400/674",12,{"$nulls":5},"3",null,null,"482","556",{"$nulls":26},"0.117028","-0.99","-0.025","1","1.1","0.069","0.172","0.12",{"$nulls":3},"Unknown",-1,"XL","Angioedema induced by ACE inhibitors, susceptibility to","General",{"$nulls":3},"C3806711","0/0","607,0","0","607","0/1","677,37","0.0518","714",null,"chrX:129754564:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0504"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZAN","chr7:100752409","ZAN(I768M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds in a species-specific manner to the zona pellucida of the egg. May be involved in gamete recognition and/or signaling.; ",{"$nulls":4},"p.Ile768Met","c.2304C>G","MODERATE","768/2812",14,{"$nulls":5},"3","433","267","315","206",null,null,"0","0",{"$nulls":22},"-0.266456",".;.;.;-0.23","2.28","1;1;1;0.999998",".;.;.;-1.29","0.879;.;0.879;.",null,"0.086;0.102;0.083;0.085",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","406,0","0","406","0/1","222,38","0.1462","260",null,"chr7:100752409:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1408"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZDHHC8","chr22:20143681","ZDHHC8(S684F)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Palmitoyltransferase involved in glutamatergic transmission. Mediates palmitoylation of ABCA1. {ECO:0000269|PubMed:19556522}.; ",{"$nulls":4},"p.Ser684Phe","c.2051C>T","MODERATE","684/778",10,{"$nulls":5},"5","329","210","210","129","296","184","0","0","0","0.2337",{"$nulls":20},"2.679606","1.04;-0.96;0.71","2.11;.;2.11","0.999969","-2.64;-2.5;-2.6","0.891;0.281;0.003","0.0","0.701;0.764;0.778",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","313,0","0","313","0/1","152,48","0.24","200",null,"chr22:20143681:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.2171"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZDHHC8","chr22:20143681","ZDHHC8(S684F)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Palmitoyltransferase involved in glutamatergic transmission. Mediates palmitoylation of ABCA1. {ECO:0000269|PubMed:19556522}.; ",{"$nulls":4},"p.Ser684Phe","c.2051C>T","MODERATE","684/778",10,{"$nulls":5},"4","329","334","210","219","297","279","0","0","0","0.0789",{"$nulls":20},"2.679606","1.04;-0.96;0.71","2.11;.;2.11","0.999969","-2.64;-2.5;-2.6","0.891;0.281;0.003","0.0","0.701;0.764;0.778",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","294,0","0","294","0/1","295,24","0.0752","319",null,"chr22:20143681:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0731"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF107","chr7:64691278","ZNF107(E12Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu12Gln","c.34G>C","MODERATE","12/852",2,{"$nulls":5},"5","582","617","424","436","484","485","0","0","0","0.0969",{"$nulls":20},"2.362197",null,null,"0.99996",{"$nulls":3},"0.324;0.333",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","537,0","0","537","0/1","521,50","0.0876","571",null,"chr7:64691278:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.0849"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF107","chr7:64691278","ZNF107(E12Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu12Gln","c.34G>C","MODERATE","12/852",2,{"$nulls":5},"5","582","729","424","529","485","583","0","0","0","0.0617",{"$nulls":20},"2.362197",null,null,"0.99996",{"$nulls":3},"0.324;0.333",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","537,0","0","537","0/1","657,43","0.0614","700",null,"chr7:64691278:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.051"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF292","chr6:87256940","ZNF292(G1104A)",null,null,"zinc finger region (C2H2-type 7 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Gly1104Ala","c.3311G>C","MODERATE","1104/2723",8,{"$nulls":5},"5","353","382","257","293","291","306","0","0","0","0.1536",{"$nulls":20},"3.085094","2.99;3.01","2.215;.","0.884384","-2.25","0.999;.","0.014","0.641;0.655",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","340,0","0","340","0/1","312,57","0.1545","369",null,"chr6:87256940:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1433"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF292","chr6:87256940","ZNF292(G1104A)",null,null,"zinc finger region (C2H2-type 7 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Gly1104Ala","c.3311G>C","MODERATE","1104/2723",8,{"$nulls":5},"5","353","385","257","302","291","315","0","0","0","0.0603",{"$nulls":20},"3.085094","2.99;3.01","2.215;.","0.884384","-2.25","0.999;.","0.014","0.641;0.655",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","335,0","0","335","0/1","352,20","0.0538","372",null,"chr6:87256940:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0596"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF302","chr19:34685050","ZNF302(E417G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu417Gly","c.1250A>G","MODERATE","417/478",7,{"$nulls":5},"5","269","331","217","252","205","250","0","0","0","0.088",{"$nulls":20},"3.843904",".;.;1.66;1.66;1.66;1.66",null,"0.720402",".;.;-6.73;-6.73;-6.73;-6.73",".;.;1.0;1.0;1.0;0.99",".;.;0.001;0.001;0.001;0.0","0.369;0.377;0.34;0.386;0.377;0.383",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","270,0","0","270","0/1","295,33","0.1006","328",null,"chr19:34685050:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.119"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF302","chr19:34685050","ZNF302(E417G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu417Gly","c.1250A>G","MODERATE","417/478",7,{"$nulls":5},"5","269","323","217","247","205","242","0","0","0","0.0909",{"$nulls":20},"3.843904",".;.;1.66;1.66;1.66;1.66",null,"0.720402",".;.;-6.73;-6.73;-6.73;-6.73",".;.;1.0;1.0;1.0;0.99",".;.;0.001;0.001;0.001;0.0","0.369;0.377;0.34;0.386;0.377;0.383",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","269,0","0","269","0/1","287,32","0.1003","319",null,"chr19:34685050:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.085"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF488","chr10:47368557","ZNF488(P91fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcriptional repressor. Plays a role in oligodendrocyte differentiation, together with OLIG2. Mediates Notch signaling-activated formation of oligodendrocyte precursors. Promotes differentiation of adult neural stem progenitor cells (NSPCs) into mature oligodendrocytes and contributes to remyelination following nerve injury. {ECO:0000250|UniProtKB:Q5HZG9}.; ",{"$nulls":4},"p.Pro91fs","c.272delC","HIGH","91/340",2,{"$nulls":5},"5","269","362","212","276","226","304","0","0","0","0.1579",{"$nulls":5},"(ZNF488|ENSG00000265763|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","245,0","0","245","0/1","261,52","0.1661","313",null,"chr10:47368557:CG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1522"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF488","chr10:47368557","ZNF488(P91fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcriptional repressor. Plays a role in oligodendrocyte differentiation, together with OLIG2. Mediates Notch signaling-activated formation of oligodendrocyte precursors. Promotes differentiation of adult neural stem progenitor cells (NSPCs) into mature oligodendrocytes and contributes to remyelination following nerve injury. {ECO:0000250|UniProtKB:Q5HZG9}.; ",{"$nulls":4},"p.Pro91fs","c.272delC","HIGH","91/340",2,{"$nulls":5},"4",null,null,"212","304","226","349",null,null,"0","0.0774",{"$nulls":5},"(ZNF488|ENSG00000265763|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","245,0","0","245","0/1","331,30","0.0831","361",null,"chr10:47368557:CG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0789"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF518A","chr10:96159244","ZNF518A(K974N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys974Asn","c.2922G>C","MODERATE","974/1483",6,{"$nulls":5},"5","405","344","298","269","355","295","0","0","0","0.0983",{"$nulls":20},"2.598544",null,"2.255",null,null,"0.005",null,"0.372;0.43;0.451",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","397,0","0","397","0/1","301,37","0.1095","338",null,"chr10:96159244:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1264"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF518A","chr10:96159244","ZNF518A(K974N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys974Asn","c.2922G>C","MODERATE","974/1483",6,{"$nulls":5},"5","405","434","298","314","355","384","0","0","0","0.0755",{"$nulls":20},"2.598544",null,"2.255",null,null,"0.005",null,"0.372;0.43;0.451",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","400,0","0","400","0/1","391,35","0.0822","426",null,"chr10:96159244:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.086"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF587B","chr19:57841520","ZNF587B(K282N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation. {ECO:0000305}.; ",{"$nulls":4},"p.Lys282Asn","c.846G>C","MODERATE","282/633",3,{"$nulls":5},"3","249","150","209","118",null,null,"0","0",{"$nulls":22},"-0.215548","5.44",".;1.43;.",null,".;-1.52;.",".;0.33;.",".;0.318;.",".;0.039;0.109",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","249,0","0","249","0/1","128,15","0.1049","143",null,"chr19:57841520:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1271"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF611","chr19:52706742","ZNF611(E105Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu105Gln","c.313G>C","MODERATE","105/705",7,{"$nulls":5},"5","407","289","334","242","303","225","0","0","0","0.2089",{"$nulls":20},"0.00459","2.77;3.06;3.06;2.77;3.06;2.77;3.77;.",".;2.14;2.14;.;2.14;.;.;.","1","-2.17;-2.17;-2.17;.;-2.17;.;.;.",".;0.354;0.354;.;0.354;.;.;.","0.075;0.07;0.07;.;0.07;.;.;.","0.032;0.021;0.02;0.033;0.029;0.047;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","399,0","0","399","0/1","232,54","0.1888","286",null,"chr19:52706742:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1942"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF611","chr19:52706742","ZNF611(E105Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu105Gln","c.313G>C","MODERATE","105/705",7,{"$nulls":5},"5","407","384","334","321","303","274","0","0","0","0.0766",{"$nulls":20},"0.00459","2.77;3.06;3.06;2.77;3.06;2.77;3.77;.",".;2.14;2.14;.;2.14;.;.;.","1","-2.17;-2.17;-2.17;.;-2.17;.;.;.",".;0.354;0.354;.;0.354;.;.;.","0.075;0.07;0.07;.;0.07;.;.;.","0.032;0.021;0.02;0.033;0.029;0.047;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","399,0","0","399","0/1","348,30","0.0794","378",null,"chr19:52706742:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.081"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF616","chr19:52116513","ZNF616(E217D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu217Asp","c.651G>C","MODERATE","217/781",4,{"$nulls":5},"5","178","110","164","93","134","82","0","0","0","0.3659",{"$nulls":20},"-0.253437","1.43","1.17","0.999997",{"$nulls":3},"0.09",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,0","0","181","0/1","68,41","0.3761","109",null,"chr19:52116513:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3978"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF616","chr19:52116513","ZNF616(E217D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu217Asp","c.651G>C","MODERATE","217/781",4,{"$nulls":5},"5","178","162","164","151","134","115","0","0","0","0.2261",{"$nulls":20},"-0.253437","1.43","1.17","0.999997",{"$nulls":3},"0.09",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,0","0","181","0/1","124,37","0.2298","161",null,"chr19:52116513:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2252"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF644","chr1:90940651","ZNF644(D235H)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1307502786",-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp235His","c.703G>C","MODERATE","235/1327",3,{"$nulls":5},"5","604","665","465","493","551","594","0","0","0","0.1263",{"$nulls":20},"2.27748","6.09","1.955","0.999961;0.999961;1;1","-0.18","0.314","0.0","0.312;0.282",{"$nulls":3},"Unknown",-1,"AD","Myopia 21, autosomal dominant","Ophthalmologic",{"$nulls":3},"C3279997","0/0","589,0","0","589","0/1","558,84","0.1308","642",null,"chr1:90940651:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1379"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF644","chr1:90940651","ZNF644(D235H)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1307502786",-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp235His","c.703G>C","MODERATE","235/1327",3,{"$nulls":5},"5","604","714","465","539","551","648","0","0","0","0.071",{"$nulls":20},"2.27748","6.09","1.955","0.999961;0.999961;1;1","-0.18","0.314","0.0","0.312;0.282",{"$nulls":3},"Unknown",-1,"AD","Myopia 21, autosomal dominant","Ophthalmologic",{"$nulls":3},"C3279997","0/0","584,0","0","584","0/1","647,51","0.0731","698",null,"chr1:90940651:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0686"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF729","chr19:22313943","ZNF729(K176E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys176Glu","c.526A>G","MODERATE","176/1252",4,{"$nulls":5},"5","41","37","29","29","36","30","0","0","0","0.2667",{"$nulls":20},"1.629114","0.24","-0.31",{"$nulls":4},"0.285",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","39,0","0","39","0/1","27,10","0.2703","37",null,"chr19:22313943:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.3103"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF729","chr19:22313943","ZNF729(K176E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys176Glu","c.526A>G","MODERATE","176/1252",4,{"$nulls":5},"5","41","37","29","32","36","39","0","0","0","0.1538",{"$nulls":20},"1.629114","0.24","-0.31",{"$nulls":4},"0.285",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","39,0","0","39","0/1","33,6","0.1538","39",null,"chr19:22313943:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1562"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF775","chr7:150397822","ZNF775(I447M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ile447Met","c.1341C>G","MODERATE","447/537",3,{"$nulls":5},"5","894","1005","679","773","559","664","0","0","0","0.1566",{"$nulls":20},"2.629754","4.7","1.795","0.973697","-1.17","0.978","0.108","0.417",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","826,0","0","826","0/1","823,133","0.1391","956",null,"chr7:150397822:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1358"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF775","chr7:150397822","ZNF775(I447M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ile447Met","c.1341C>G","MODERATE","447/537",3,{"$nulls":5},"5","894","1151","679","901","561","723","0","0","0","0.0595",{"$nulls":20},"2.629754","4.7","1.795","0.973697","-1.17","0.978","0.108","0.417",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","825,0","0","825","0/1","1023,60","0.0554","1083",null,"chr7:150397822:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF778","chr16:89223218","ZNF778(D60G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.; ",{"$nulls":4},"p.Asp60Gly","c.179A>G","MODERATE","60/757",4,{"$nulls":5},"5","540","374","374","265","472","329","0","0","0","0.1246",{"$nulls":20},"1.856421","4.23;4.23;.",null,"1;0.999186","-4.66;-6.1;.",".;.;0.921","0.014;0.004;.","0.316;.;0.278",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","507,0","0","507","0/1","312,44","0.1236","356",null,"chr16:89223218:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1208"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF778","chr16:89223218","ZNF778(D60G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.; ",{"$nulls":4},"p.Asp60Gly","c.179A>G","MODERATE","60/757",4,{"$nulls":5},"5","540","514","374","358","470","432","0","0","0","0.0671",{"$nulls":20},"1.856421","4.23;4.23;.",null,"1;0.999186","-4.66;-6.1;.",".;.;0.921","0.014;0.004;.","0.316;.;0.278",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","514,0","0","514","0/1","447,33","0.0688","480",null,"chr16:89223218:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0698"]
["01TL","T10","JLPIKTOR_JLPIKTOR_17113001TL","ZNF91","chr19:23361877","ZNF91(H368D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor specifically required to repress SINE-VNTR-Alu (SVA) retrotransposons: recognizes and binds SVA sequences and represses their expression by recruiting a repressive complex containing TRIM28/KAP1 (PubMed:25274305). May also bind the promoter of the FCGR2B gene, leading to repress its expression; however, additional evidences are required to confirm this result in vivo (PubMed:11470777). {ECO:0000269|PubMed:25274305, ECO:0000305|PubMed:11470777}.; ",{"$nulls":4},"p.His368Asp","c.1102C>G","MODERATE","368/1191",4,1,{"$nulls":4},"3","398","289","308","218",null,null,"0","0",{"$nulls":22},"2.419549","-2.17","4.325;.","0.935165","-7.6;-7.05","0.996","0.0","0.297;0.322",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","391,0","0","391","0/1","231,52","0.1837","283",null,"chr19:23361877:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf","unknown","PASS","tumor","significant","0.1697"]
["01TL","T9_","JLPIKTOR_JLPIKTOR_17113001TL","ZNF91","chr19:23361877","ZNF91(H368D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor specifically required to repress SINE-VNTR-Alu (SVA) retrotransposons: recognizes and binds SVA sequences and represses their expression by recruiting a repressive complex containing TRIM28/KAP1 (PubMed:25274305). May also bind the promoter of the FCGR2B gene, leading to repress its expression; however, additional evidences are required to confirm this result in vivo (PubMed:11470777). {ECO:0000269|PubMed:25274305, ECO:0000305|PubMed:11470777}.; ",{"$nulls":4},"p.His368Asp","c.1102C>G","MODERATE","368/1191",4,1,{"$nulls":4},"3",null,null,"308","279",{"$nulls":26},"2.419549","-2.17","4.325;.","0.935165","-7.6;-7.05","0.996","0.0","0.297;0.322",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","389,0","0","389","0/1","341,27","0.0734","368",null,"chr19:23361877:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113001TL","somatic","somatic","JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113001TL/somatic/JLPIKTOR_17113001TL_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113001TL_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0753"]

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["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","AASDHPPT","chr11:106091373","AASDHPPT(R197G)",null,null,"splice variant (In isoform 2. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the post-translational modification of target proteins by phosphopantetheine. Can transfer the 4'- phosphopantetheine moiety from coenzyme A to a serine residue of a broad range of acceptors, such as the acyl carrier domain of FASN. {ECO:0000269|PubMed:11286508, ECO:0000269|PubMed:12815048, ECO:0000269|PubMed:18022563}.; ",{"$nulls":4},"p.Arg197Gly","c.589C>G","MODERATE","197/309",4,{"$nulls":5},"5","375","152","321","127","313","135","0","0","0","0.1037",{"$nulls":20},"3.252992",null,".;.;2.135","0.960676","-5.11;-4.78;-4.58",".;.;0.992","0.069;0.044;0.013",".;.;0.797",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is similar to Saccharomyces cerevisiae LYS5, which is required for the activation of the alpha-aminoadipate dehydrogenase in the biosynthetic pathway of lysine. Yeast alpha-aminoadipate dehydrogenase converts alpha-biosynthetic-aminoadipate semialdehyde to alpha-aminoadipate. It has been suggested that defects in the human gene result in pipecolic acidemia. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","373,0","0","373","0/1","134,17","0.1126","151",null,"chr11:106091373:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0945"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","AASDHPPT","chr11:106091373","AASDHPPT(R197G)",null,null,"splice variant (In isoform 2. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the post-translational modification of target proteins by phosphopantetheine. Can transfer the 4'- phosphopantetheine moiety from coenzyme A to a serine residue of a broad range of acceptors, such as the acyl carrier domain of FASN. {ECO:0000269|PubMed:11286508, ECO:0000269|PubMed:12815048, ECO:0000269|PubMed:18022563}.; ",{"$nulls":4},"p.Arg197Gly","c.589C>G","MODERATE","197/309",4,{"$nulls":5},"5","375","127","321","107","313","108","0","0","0","0.3796",{"$nulls":20},"3.252992",null,".;.;2.135","0.960676","-5.11;-4.78;-4.58",".;.;0.992","0.069;0.044;0.013",".;.;0.797",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is similar to Saccharomyces cerevisiae LYS5, which is required for the activation of the alpha-aminoadipate dehydrogenase in the biosynthetic pathway of lysine. Yeast alpha-aminoadipate dehydrogenase converts alpha-biosynthetic-aminoadipate semialdehyde to alpha-aminoadipate. It has been suggested that defects in the human gene result in pipecolic acidemia. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","373,0","0","373","0/1","77,46","0.374","123",null,"chr11:106091373:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3832"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ABCA6","chr17:69137450","ABCA6(S49R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable transporter which may play a role in macrophage lipid homeostasis.; ",{"$nulls":4},"p.Ser49Arg","c.147T>A","MODERATE","49/1617",3,{"$nulls":5},"5","261","157","189","120","250","142","0","0","0","0.3028",{"$nulls":20},"0.683325","-2.36;0.87","0.83","1","-1.18;.","0.003;0.011","0.444;.","0.163;0.154",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","261,0","0","261","0/1","104,49","0.3203","153",null,"chr17:69137450:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3333"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ACOX1","chr17:75960265","ACOX1(A127V)",null,null,"splice variant (In isoform 2 and isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the desaturation of acyl-CoAs to 2-trans- enoyl-CoAs. Isoform 1 shows highest activity against medium-chain fatty acyl-CoAs and activity decreases with increasing chain length. Isoform 2 is active against a much broader range of substrates and shows activity towards very long-chain acyl-CoAs. Isoform 2 is twice as active as isoform 1 against 16-hydroxy- palmitoyl-CoA and is 25% more active against 1,16-hexadecanodioyl- CoA. {ECO:0000269|PubMed:17458872, ECO:0000269|PubMed:17603022}.; ","level2",{"$nulls":3},"p.Ala127Val","c.380C>T","MODERATE","127/660",3,{"$nulls":5},"5","653","457","485","310","555","380","0","0","0","0.2921",{"$nulls":20},"3.449191","0.46",null,"0.999997;0.999997;0.999997;0.999997;1","-3.27","0.007","0.023","0.621",{"$nulls":3},"Unknown",-1,"AR","Peroxisomal acyl-CoA oxidase deficiency","Audiologic/Otolaryngologic; Biochemical; Craniofacial; Neurologic; Ophthalmologic",{"$nulls":3},"C1849678","0/0","637,0","0","637","0/1","315,117","0.2708","432",null,"chr17:75960265:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2839"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ACOX1","chr17:75960265","ACOX1(A127V)",null,null,"splice variant (In isoform 2 and isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the desaturation of acyl-CoAs to 2-trans- enoyl-CoAs. Isoform 1 shows highest activity against medium-chain fatty acyl-CoAs and activity decreases with increasing chain length. Isoform 2 is active against a much broader range of substrates and shows activity towards very long-chain acyl-CoAs. Isoform 2 is twice as active as isoform 1 against 16-hydroxy- palmitoyl-CoA and is 25% more active against 1,16-hexadecanodioyl- CoA. {ECO:0000269|PubMed:17458872, ECO:0000269|PubMed:17603022}.; ","level2",{"$nulls":3},"p.Ala127Val","c.380C>T","MODERATE","127/660",3,{"$nulls":5},"5","653","451","485","314","555","397","0","0","0","0.3476",{"$nulls":20},"3.449191","0.46",null,"0.999997;0.999997;0.999997;0.999997;1","-3.27","0.007","0.023","0.621",{"$nulls":3},"Unknown",-1,"AR","Peroxisomal acyl-CoA oxidase deficiency","Audiologic/Otolaryngologic; Biochemical; Craniofacial; Neurologic; Ophthalmologic",{"$nulls":3},"C1849678","0/0","632,0","0","632","0/1","271,148","0.3532","419",null,"chr17:75960265:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3185"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ACTR2","chr2:65261380","ACTR2(D295A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: ATP-binding component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation-promoting factor (NPF) (PubMed:9000076). The Arp2/3 complex mediates the formation of branched actin networks in the cytoplasm, providing the force for cell motility (PubMed:9000076). Seems to contact the pointed end of the daughter actin filament (PubMed:9000076). In addition to its role in the cytoplasmic cytoskeleton, the Arp2/3 complex also promotes actin polymerization in the nucleus, thereby regulating gene transcription and repair of damaged DNA (PubMed:17220302, PubMed:29925947). The Arp2/3 complex promotes homologous recombination (HR) repair in response to DNA damage by promoting nuclear actin polymerization, leading to drive motility of double- strand breaks (DSBs) (PubMed:29925947). {ECO:0000269|PubMed:17220302, ECO:0000269|PubMed:29925947, ECO:0000269|PubMed:9000076}.; ",{"$nulls":4},"p.Asp295Ala","c.884A>C","MODERATE","295/399",8,{"$nulls":5},"5","429","248","316","183","360","220","0","0","0","0.2455",{"$nulls":20},"3.880249","2.91","3.105;.;.","1","-5.58;-5.58;-5.84","0.973;.;0.753","0.041;0.042;0.044","0.809;0.8;0.807",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","421,0","0","421","0/1","180,68","0.2742","248",null,"chr2:65261380:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2896"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ADAMTSL1","chr9:18777650","ADAMTSL1(F1141V)",null,null,"splice variant (In isoform 5 and isoform 6. ), splice variant (In isoform 2. ), splice variant (In isoform 1. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe1141Val","c.3421T>G","MODERATE","1141/1762",19,{"$nulls":5},"5","1044","537","817","402","859","440","0.001","0.001","0","0.4477",{"$nulls":20},"2.63989","0.08","0.55","0.911767","-0.98","0.146","0.504","0.681",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1020,1","0.001","1021","0/1","294,224","0.4324","518",null,"chr9:18777650:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4279"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","AKNA","chr9:114337281","AKNA(S1365A)",null,null,"splice variant (In isoform 6. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that specifically activates the expression of the CD40 receptor and its ligand CD40L/CD154, two cell surface molecules on lymphocytes that are critical for antigen-dependent-B-cell development. Binds to A/T-rich promoters. {ECO:0000269|PubMed:11268217}.; ",{"$nulls":4},"p.Ser1365Ala","c.4093T>G","MODERATE","1365/1439",22,{"$nulls":5},"5","582","221","447","156","517","190","0","0","0","0.5316",{"$nulls":20},"3.02714","1.39;1.39;1.41;1.12;1.36","2.045;2.045;.;.;.","0.868624","-1.61;-1.61;-2.11;-1.53;-1.61","0.999;0.999;.;.;0.999","0.105;0.105;0.201;0.13;0.106","0.102;0.088;0.081;0.103;0.076",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","581,0","0","581","0/1","98,118","0.5463","216",null,"chr9:114337281:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5513"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ALMS1","chr2:73385888","ALMS1(P7L)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Alstrom syndrome (ALMS) [MIM:203800]: A rare autosomal recessive disorder characterized by progressive cone-rod retinal dystrophy, neurosensory hearing loss, early childhood obesity and diabetes mellitus type 2. Dilated cardiomyopathy, acanthosis nigricans, male hypogonadism, hypothyroidism, developmental delay and hepatic dysfunction can also be associated with the syndrome. {ECO:0000269|PubMed:11941369, ECO:0000269|PubMed:11941370}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in PCM1-dependent intracellular transport. Required, directly or indirectly, for the localization of NCAPD2 to the proximal ends of centrioles. Required for proper formation and/or maintenance of primary cilia (PC), microtubule-based structures that protrude from the surface of epithelial cells. {ECO:0000269|PubMed:17954613}.; ",{"$nulls":4},"p.Pro7Leu","c.20C>T","MODERATE","7/4168",1,{"$nulls":5},"4","153","103","141","98",null,null,"0","0",{"$nulls":22},"3.3508459999999998",null,".;1.75;.","0.77487",null,".;1.0;.",null,"0.61;0.609;0.62",{"$nulls":3},"Unknown",-1,"AR","Alstrom syndrome","Audiologic/Otolaryngologic; Cardiovascular; Endocrine; Gastrointestinal; Ophthalmologic; Renal",{"$nulls":3},"C0268425","0/0","146,0","0","146","0/1","77,21","0.2143","98",null,"chr2:73385888:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1939"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ALMS1","chr2:73385888","ALMS1(P7L)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Alstrom syndrome (ALMS) [MIM:203800]: A rare autosomal recessive disorder characterized by progressive cone-rod retinal dystrophy, neurosensory hearing loss, early childhood obesity and diabetes mellitus type 2. Dilated cardiomyopathy, acanthosis nigricans, male hypogonadism, hypothyroidism, developmental delay and hepatic dysfunction can also be associated with the syndrome. {ECO:0000269|PubMed:11941369, ECO:0000269|PubMed:11941370}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in PCM1-dependent intracellular transport. Required, directly or indirectly, for the localization of NCAPD2 to the proximal ends of centrioles. Required for proper formation and/or maintenance of primary cilia (PC), microtubule-based structures that protrude from the surface of epithelial cells. {ECO:0000269|PubMed:17954613}.; ",{"$nulls":4},"p.Pro7Leu","c.20C>T","MODERATE","7/4168",1,{"$nulls":5},"5","153","101","141","89","47","48","0","0","0","0.5417",{"$nulls":20},"3.3508459999999998",null,".;1.75;.","0.77487",null,".;1.0;.",null,"0.61;0.609;0.62",{"$nulls":3},"Unknown",-1,"AR","Alstrom syndrome","Audiologic/Otolaryngologic; Cardiovascular; Endocrine; Gastrointestinal; Ophthalmologic; Renal",{"$nulls":3},"C0268425","0/0","146,0","0","146","0/1","63,30","0.3226","93",null,"chr2:73385888:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3371"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ANGEL2","chr1:213008304","ANGEL2(N183T)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asn183Thr","c.548A>C","MODERATE","183/544",3,{"$nulls":5},"5","418","423","327","313","363","343","0","0","0","0.1545",{"$nulls":20},"3.800352","2.01;1.05;1.07","1.29;.;.","1","-3.73;-3.5;-3.83","0.756;.;.","0.005;0.006;0.014","0.792;0.803;0.803",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","409,0","0","409","0/1","353,63","0.1514","416",null,"chr1:213008304:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.147"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","APOB","chr2:21002584","APOB(A4280T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hypobetalipoproteinemia, familial, 1 (FHBL1) [MIM:615558]: A disorder of lipid metabolism characterized by less than 5th percentile age- and sex-specific levels of low density lipoproteins, and dietary fat malabsorption. Clinical presentation may vary from no symptoms to severe gastrointestinal and neurological dysfunction similar to abetalipoproteinemia. {ECO:0000269|PubMed:12551903, ECO:0000269|PubMed:21981844, ECO:0000269|PubMed:27206948}. Note=The disease is caused by mutations affecting the gene represented in this entry. Most cases of FHBL1 result from nonsense mutations in the APOB gene that lead to a premature stop codon, which generate prematurely truncated apo B protein products (PubMed:21981844). {ECO:0000269|PubMed:21981844}.; DISEASE: Familial ligand-defective apolipoprotein B-100 (FDB) [MIM:144010]: Dominantly inherited disorder of lipoprotein metabolism leading to hypercholesterolemia and increased proneness to coronary artery disease (CAD). The plasma cholesterol levels are dramatically elevated due to impaired clearance of LDL particles by defective APOB/E receptors. {ECO:0000269|PubMed:21382890, ECO:0000269|PubMed:2563166, ECO:0000269|PubMed:7883971, ECO:0000269|PubMed:9259199}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in APOB associated with defects in other genes (polygenic) can contribute to hypocholesterolemia.; ","FUNCTION: Apolipoprotein B is a major protein constituent of chylomicrons (apo B-48), LDL (apo B-100) and VLDL (apo B-100). Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor.; ","acmg",{"$nulls":3},"p.Ala4280Thr","c.12838G>A","MODERATE","4280/4563",29,{"$nulls":5},"5","625","371","484","265","544","330","0","0","0","0.1242",{"$nulls":20},"0.364986","5.84",null,"1","-0.08",null,"0.254","0.023",{"$nulls":3},"Unknown",-1,"AD/AR","Hypobetalipoproteinemia, familial; Hypercholesterolemia, familial","Cardiovascular; Gastrointestinal; Hematologic; Neurologic; Ophthalmologic",null,"This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Jul 2008].  ",null,"C4551990| C1704417","0/0","619,0","0","619","0/1","310,48","0.1341","358",null,"chr2:21002584:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1321"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","APOB","chr2:21002584","APOB(A4280T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hypobetalipoproteinemia, familial, 1 (FHBL1) [MIM:615558]: A disorder of lipid metabolism characterized by less than 5th percentile age- and sex-specific levels of low density lipoproteins, and dietary fat malabsorption. Clinical presentation may vary from no symptoms to severe gastrointestinal and neurological dysfunction similar to abetalipoproteinemia. {ECO:0000269|PubMed:12551903, ECO:0000269|PubMed:21981844, ECO:0000269|PubMed:27206948}. Note=The disease is caused by mutations affecting the gene represented in this entry. Most cases of FHBL1 result from nonsense mutations in the APOB gene that lead to a premature stop codon, which generate prematurely truncated apo B protein products (PubMed:21981844). {ECO:0000269|PubMed:21981844}.; DISEASE: Familial ligand-defective apolipoprotein B-100 (FDB) [MIM:144010]: Dominantly inherited disorder of lipoprotein metabolism leading to hypercholesterolemia and increased proneness to coronary artery disease (CAD). The plasma cholesterol levels are dramatically elevated due to impaired clearance of LDL particles by defective APOB/E receptors. {ECO:0000269|PubMed:21382890, ECO:0000269|PubMed:2563166, ECO:0000269|PubMed:7883971, ECO:0000269|PubMed:9259199}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in APOB associated with defects in other genes (polygenic) can contribute to hypocholesterolemia.; ","FUNCTION: Apolipoprotein B is a major protein constituent of chylomicrons (apo B-48), LDL (apo B-100) and VLDL (apo B-100). Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor.; ","acmg",{"$nulls":3},"p.Ala4280Thr","c.12838G>A","MODERATE","4280/4563",29,{"$nulls":5},"5","625","355","484","259","544","316","0","0","0","0.307",{"$nulls":20},"0.364986","5.84",null,"1","-0.08",null,"0.254","0.023",{"$nulls":3},"Unknown",-1,"AD/AR","Hypobetalipoproteinemia, familial; Hypercholesterolemia, familial","Cardiovascular; Gastrointestinal; Hematologic; Neurologic; Ophthalmologic",null,"This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Jul 2008].  ",null,"C4551990| C1704417","0/0","621,0","0","621","0/1","247,107","0.3023","354",null,"chr2:21002584:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3243"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","APOB","chr2:21005280","APOB(E3863A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hypobetalipoproteinemia, familial, 1 (FHBL1) [MIM:615558]: A disorder of lipid metabolism characterized by less than 5th percentile age- and sex-specific levels of low density lipoproteins, and dietary fat malabsorption. Clinical presentation may vary from no symptoms to severe gastrointestinal and neurological dysfunction similar to abetalipoproteinemia. {ECO:0000269|PubMed:12551903, ECO:0000269|PubMed:21981844, ECO:0000269|PubMed:27206948}. Note=The disease is caused by mutations affecting the gene represented in this entry. Most cases of FHBL1 result from nonsense mutations in the APOB gene that lead to a premature stop codon, which generate prematurely truncated apo B protein products (PubMed:21981844). {ECO:0000269|PubMed:21981844}.; DISEASE: Familial ligand-defective apolipoprotein B-100 (FDB) [MIM:144010]: Dominantly inherited disorder of lipoprotein metabolism leading to hypercholesterolemia and increased proneness to coronary artery disease (CAD). The plasma cholesterol levels are dramatically elevated due to impaired clearance of LDL particles by defective APOB/E receptors. {ECO:0000269|PubMed:21382890, ECO:0000269|PubMed:2563166, ECO:0000269|PubMed:7883971, ECO:0000269|PubMed:9259199}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in APOB associated with defects in other genes (polygenic) can contribute to hypocholesterolemia.; ","FUNCTION: Apolipoprotein B is a major protein constituent of chylomicrons (apo B-48), LDL (apo B-100) and VLDL (apo B-100). Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor.; ","acmg",{"$nulls":3},"p.Glu3863Ala","c.11588A>C","MODERATE","3863/4563",26,1,{"$nulls":4},"4","2021","1365","1650","1060","1625","1154","0","0","0","0.3172",{"$nulls":20},"2.620232","5.62",null,"0.998046","-3.53",null,"0.005","0.256",{"$nulls":3},"Unknown",-1,"AD/AR","Hypobetalipoproteinemia, familial; Hypercholesterolemia, familial","Cardiovascular; Gastrointestinal; Hematologic; Neurologic; Ophthalmologic",null,"This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Jul 2008].  ",null,"C4551990| C1704417","0/0","1982,0","0","1982","0/1","892,415","0.3175","1307",null,"chr2:21005280:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3113"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ARIH2","chr3:48973745","ARIH2(I273V)",null,null,"region of interest (TRIAD supradomain )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase, which catalyzes ubiquitination of target proteins together with ubiquitin- conjugating enzyme E2 UBE2L3 (PubMed:16118314, PubMed:17646546, PubMed:19340006, PubMed:24076655). Acts as an atypical E3 ubiquitin-protein ligase by working together with cullin-5-RING ubiquitin ligase complex (ECS complex, also named CRL5 complex) and initiating ubiquitination of ECS substrates: associates with ECS complex and specifically mediates addition of the first ubiquitin on ECS targets (By similarity). The initial ubiquitin is then elongated (By similarity). E3 ubiquitin-protein ligase activity is activated upon binding to neddylated form of the ECS complex (PubMed:24076655). Mediates 'Lys-6', 'Lys-48'-and 'Lys- 63'-linked polyubiquitination (PubMed:16118314, PubMed:17646546, PubMed:19340006). May play a role in myelopoiesis (PubMed:19340006). {ECO:0000250|UniProtKB:Q9Y4X5, ECO:0000269|PubMed:16118314, ECO:0000269|PubMed:17646546, ECO:0000269|PubMed:19340006, ECO:0000269|PubMed:24076655}.; ",{"$nulls":4},"p.Ile273Val","c.817A>G","MODERATE","273/493",9,{"$nulls":5},"5","659","345","457","230","587","289","0","0","0","0.1246",{"$nulls":20},"2.875784","0.04","-0.85","1","-0.84","0.05","0.063","0.406;0.404",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","622,0","0","622","0/1","278,43","0.134","321",null,"chr3:48973745:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1261"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ARIH2","chr3:48973745","ARIH2(I273V)",null,null,"region of interest (TRIAD supradomain )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase, which catalyzes ubiquitination of target proteins together with ubiquitin- conjugating enzyme E2 UBE2L3 (PubMed:16118314, PubMed:17646546, PubMed:19340006, PubMed:24076655). Acts as an atypical E3 ubiquitin-protein ligase by working together with cullin-5-RING ubiquitin ligase complex (ECS complex, also named CRL5 complex) and initiating ubiquitination of ECS substrates: associates with ECS complex and specifically mediates addition of the first ubiquitin on ECS targets (By similarity). The initial ubiquitin is then elongated (By similarity). E3 ubiquitin-protein ligase activity is activated upon binding to neddylated form of the ECS complex (PubMed:24076655). Mediates 'Lys-6', 'Lys-48'-and 'Lys- 63'-linked polyubiquitination (PubMed:16118314, PubMed:17646546, PubMed:19340006). May play a role in myelopoiesis (PubMed:19340006). {ECO:0000250|UniProtKB:Q9Y4X5, ECO:0000269|PubMed:16118314, ECO:0000269|PubMed:17646546, ECO:0000269|PubMed:19340006, ECO:0000269|PubMed:24076655}.; ",{"$nulls":4},"p.Ile273Val","c.817A>G","MODERATE","273/493",9,{"$nulls":5},"5","659","325","457","223","588","278","0","0","0","0.536",{"$nulls":20},"2.875784","0.04","-0.85","1","-0.84","0.05","0.063","0.406;0.404",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","623,0","0","623","0/1","141,151","0.5171","292",null,"chr3:48973745:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5022"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ATF1","chr12:50819700","ATF1(A246V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Angiomatoid fibrous histiocytoma (AFH) [MIM:612160]: A distinct variant of malignant fibrous histiocytoma that typically occurs in children and adolescents and is manifest by nodular subcutaneous growth. Characteristic microscopic features include lobulated sheets of histiocyte-like cells intimately associated with areas of hemorrhage and cystic pseudovascular spaces, as well as a striking cuffing of inflammatory cells, mimicking a lymph node metastasis. Note=The gene represented in this entry may be involved in disease pathogenesis. Chromosomal aberrations involving ATF1 are found in patients with angiomatoid fibrous histiocytoma. Translocation t(12;16)(q13;p11.2) with FUS generates a chimeric ATF1/FUS protein. Translocation t(12;22)(q13;q12) with EWSR1 generates a chimeric ATF1/EWSR1 protein.; ","FUNCTION: This protein binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Binds to the Tax-responsive element (TRE) of HTLV-I. Mediates PKA-induced stimulation of CRE-reporter genes. Represses the expression of FTH1 and other antioxidant detoxification genes. Triggers cell proliferation and transformation. {ECO:0000269|PubMed:18794154, ECO:0000269|PubMed:20980392}.; ","gedi|level2",{"$nulls":3},"p.Ala246Val","c.737C>T","MODERATE","246/271",7,{"$nulls":5},"4","77","29","53","22",null,null,"0","0",{"$nulls":22},"3.06748","0.36","1.825","1","-3.26","0.543","0.046","0.708",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","75,0","0","75","0/1","24,5","0.1724","29",null,"chr12:50819700:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1364"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ATF1","chr12:50819700","ATF1(A246V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Angiomatoid fibrous histiocytoma (AFH) [MIM:612160]: A distinct variant of malignant fibrous histiocytoma that typically occurs in children and adolescents and is manifest by nodular subcutaneous growth. Characteristic microscopic features include lobulated sheets of histiocyte-like cells intimately associated with areas of hemorrhage and cystic pseudovascular spaces, as well as a striking cuffing of inflammatory cells, mimicking a lymph node metastasis. Note=The gene represented in this entry may be involved in disease pathogenesis. Chromosomal aberrations involving ATF1 are found in patients with angiomatoid fibrous histiocytoma. Translocation t(12;16)(q13;p11.2) with FUS generates a chimeric ATF1/FUS protein. Translocation t(12;22)(q13;q12) with EWSR1 generates a chimeric ATF1/EWSR1 protein.; ","FUNCTION: This protein binds the cAMP response element (CRE) (consensus: 5'-GTGACGT[AC][AG]-3'), a sequence present in many viral and cellular promoters. Binds to the Tax-responsive element (TRE) of HTLV-I. Mediates PKA-induced stimulation of CRE-reporter genes. Represses the expression of FTH1 and other antioxidant detoxification genes. Triggers cell proliferation and transformation. {ECO:0000269|PubMed:18794154, ECO:0000269|PubMed:20980392}.; ","gedi|level2",{"$nulls":3},"p.Ala246Val","c.737C>T","MODERATE","246/271",7,{"$nulls":5},"5","77","47","53","38","67","42","0","0","0","0.3095",{"$nulls":20},"3.06748","0.36","1.825","1","-3.26","0.543","0.046","0.708",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","75,0","0","75","0/1","35,13","0.2708","48",null,"chr12:50819700:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3158"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","BTK","chrX:101357551","BTK(Q413E)",null,null,"domain (Protein kinase ), nucleotide phosphate-binding region (ATP ), turn ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: X-linked agammaglobulinemia (XLA) [MIM:300755]: Humoral immunodeficiency disease which results in developmental defects in the maturation pathway of B-cells. Affected boys have normal levels of pre-B-cells in their bone marrow but virtually no circulating mature B-lymphocytes. This results in a lack of immunoglobulins of all classes and leads to recurrent bacterial infections like otitis, conjunctivitis, dermatitis, sinusitis in the first few years of life, or even some patients present overwhelming sepsis or meningitis, resulting in death in a few hours. Treatment in most cases is by infusion of intravenous immunoglobulin. {ECO:0000269|PubMed:10220140, ECO:0000269|PubMed:10612838, ECO:0000269|PubMed:10678660, ECO:0000269|PubMed:7627183, ECO:0000269|PubMed:7633420, ECO:0000269|PubMed:7633429, ECO:0000269|PubMed:7711734, ECO:0000269|PubMed:7809124, ECO:0000269|PubMed:7849006, ECO:0000269|PubMed:7849697, ECO:0000269|PubMed:7849721, ECO:0000269|PubMed:7880320, ECO:0000269|PubMed:7897635, ECO:0000269|PubMed:8013627, ECO:0000269|PubMed:8162018, ECO:0000269|PubMed:8162056, ECO:0000269|PubMed:8594569, ECO:0000269|PubMed:8634718, ECO:0000269|PubMed:8695804, ECO:0000269|PubMed:8723128, ECO:0000269|PubMed:8834236, ECO:0000269|PubMed:9016530, ECO:0000269|PubMed:9260159, ECO:0000269|PubMed:9280283, ECO:0000269|PubMed:9445504, ECO:0000269|PubMed:9545398}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: X-linked hypogammaglobulinemia and isolated growth hormone deficiency (XLA-IGHD) [MIM:307200]: In rare cases XLA is inherited together with isolated growth hormone deficiency (IGHD). {ECO:0000269|PubMed:8013627}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Non-receptor tyrosine kinase indispensable for B lymphocyte development, differentiation and signaling. Binding of antigen to the B-cell antigen receptor (BCR) triggers signaling that ultimately leads to B-cell activation. After BCR engagement and activation at the plasma membrane, phosphorylates PLCG2 at several sites, igniting the downstream signaling pathway through calcium mobilization, followed by activation of the protein kinase C (PKC) family members. PLCG2 phosphorylation is performed in close cooperation with the adapter protein B-cell linker protein BLNK. BTK acts as a platform to bring together a diverse array of signaling proteins and is implicated in cytokine receptor signaling pathways. Plays an important role in the function of immune cells of innate as well as adaptive immunity, as a component of the Toll-like receptors (TLR) pathway. The TLR pathway acts as a primary surveillance system for the detection of pathogens and are crucial to the activation of host defense. Especially, is a critical molecule in regulating TLR9 activation in splenic B-cells. Within the TLR pathway, induces tyrosine phosphorylation of TIRAP which leads to TIRAP degradation. BTK plays also a critical role in transcription regulation. Induces the activity of NF-kappa-B, which is involved in regulating the expression of hundreds of genes. BTK is involved on the signaling pathway linking TLR8 and TLR9 to NF-kappa-B. Transiently phosphorylates transcription factor GTF2I on tyrosine residues in response to BCR. GTF2I then translocates to the nucleus to bind regulatory enhancer elements to modulate gene expression. ARID3A and NFAT are other transcriptional target of BTK. BTK is required for the formation of functional ARID3A DNA-binding complexes. There is however no evidence that BTK itself binds directly to DNA. BTK has a dual role in the regulation of apoptosis. {ECO:0000269|PubMed:11606584, ECO:0000269|PubMed:16415872, ECO:0000269|PubMed:16517732, ECO:0000269|PubMed:16738337, ECO:0000269|PubMed:17932028, ECO:0000269|PubMed:9012831}.; ","gedi|foundationOne","[ \"Dasatinib\" , \"Ibrutinib\"]","[ \"Dasatinib\" , \"Ibrutinib\"]","[ \"Dasatinib\" , \"Ibrutinib\"]","p.Gln413Glu","c.1237C>G","MODERATE","413/693",13,{"$nulls":5},"5","532","330","387","230","479","293","0","0","0","0.058",{"$nulls":20},"1.481509",".;.;-0.89",".;.;0.805","1;0.999151",".;.;-0.31",".;.;0.001",".;.;1.0","0.199;0.18;0.173",{"$nulls":3},"Unknown",-1,"XL","Agammaglobulinemia, X-linked; Agammaglobulinemia and isolated hormone deficiency; Hypogammaglobulinemia, X-linked","Allergy/Immunology/Infectious",{"$nulls":3},"C0221026| C0472813","0/0","522,0","0","522","0/1","293,22","0.0698","315",null,"chrX:101357551:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0696"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","C2CD2","chr21:41907677","C2CD2(G376C)",{"$nulls":6},255,"PASS","Missense","rs778367156",-1,{"$nulls":6},"p.Gly376Cys","c.1126G>T","MODERATE","376/696",9,{"$nulls":5},"5","390","265","331","215","300","208","0","0","0","0.0673",{"$nulls":20},"3.542223","-1.25",null,"1","-4.63;-5.3",".;1.0","0.012;0.007","0.958;0.932",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","386,0","0","386","0/1","245,17","0.0649","262",null,"chr21:41907677:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0651"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","C5orf24","chr5:134855346","C5orf24(S149F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser149Phe","c.446C>T","MODERATE","149/188",2,1,{"$nulls":4},"5","453","242","348","174","394","199","0","0","0","0.1457",{"$nulls":20},"3.8948739999999997",null,"1.935","1","-1.78","0.997","0.054","0.66;0.661;0.775",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","448,0","0","448","0/1","202,38","0.1583","240",null,"chr5:134855346:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1724"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CAPN1","chr11:65188428","CAPN1(N315T)",null,null,"domain (Calpain catalytic ), calcium-binding region (2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Spastic paraplegia 76, autosomal recessive (SPG76) [MIM:616907]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269|PubMed:27153400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. {ECO:0000269|PubMed:21531719, ECO:0000269|PubMed:2400579}.; ","level2",{"$nulls":3},"p.Asn315Thr","c.944A>C","MODERATE","315/714",9,{"$nulls":5},"4","552","353","486","299","439","279","0.0054","0.0054","0","0.405",{"$nulls":20},"2.476126","2.33","1.46","0.999021","-3.6","0.0","0.063","0.308;0.307;0.305;0.306;0.305",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS","The calpains, calcium-activated neutral proteases, are nonlysosomal, intracellular cysteine proteases. The mammalian calpains include ubiquitous, stomach-specific, and muscle-specific proteins. The ubiquitous enzymes consist of heterodimers with distinct large, catalytic subunits associated with a common small, regulatory subunit. This gene encodes the large subunit of the ubiquitous enzyme, calpain 1. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Nov 2010].",null,"C4310800","0/0","546,3","0.0055","549","0/1","222,122","0.3547","344",null,"chr11:65188428:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3645"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CCDC94","chr19:4262088","CCDC94(P228S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro228Ser","c.682C>T","MODERATE","228/323",6,1,{"$nulls":4},"5","337","175","239","120","287","146","0","0","0","0.089",{"$nulls":20},"1.229679","1.65",null,"0.999809","0.1","0.023","0.241","0.072",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","333,0","0","333","0/1","151,18","0.1065","169",null,"chr19:4262088:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1083"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CCDC94","chr19:4262088","CCDC94(P228S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro228Ser","c.682C>T","MODERATE","228/323",6,1,{"$nulls":4},"5","337","287","239","196","287","253","0","0","0","0.2925",{"$nulls":20},"1.229679","1.65",null,"0.999809","0.1","0.023","0.241","0.072",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","333,0","0","333","0/1","191,93","0.3275","284",null,"chr19:4262088:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3367"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CD163","chr12:7501159","CD163(D146V)",null,null,"topological domain (Extracellular ), domain (SRCR 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs905885266",-1,null,"FUNCTION: Acute phase-regulated receptor involved in clearance and endocytosis of hemoglobin/haptoglobin complexes by macrophages and may thereby protect tissues from free hemoglobin-mediated oxidative damage. May play a role in the uptake and recycling of iron, via endocytosis of hemoglobin/haptoglobin and subsequent breakdown of heme. Binds hemoglobin/haptoglobin complexes in a calcium-dependent and pH-dependent manner. Exhibits a higher affinity for complexes of hemoglobin and multimeric haptoglobin of HP*1F phenotype than for complexes of hemoglobin and dimeric haptoglobin of HP*1S phenotype. Induces a cascade of intracellular signals that involves tyrosine kinase-dependent calcium mobilization, inositol triphosphate production and secretion of IL6 and CSF1. Isoform 3 exhibits the higher capacity for ligand endocytosis and the more pronounced surface expression when expressed in cells.; ",{"$nulls":4},"p.Asp146Val","c.437A>T","MODERATE","146/1156",3,{"$nulls":5},"5","660","433","496","305","577","374","0","0","0","0.131",{"$nulls":20},"4.057871","1.21","2.935;.;.;2.935","1","-4.84;-4.85;-5.34;-4.69","1.0;.;1.0;1.0","0.046;0.048;0.04;0.045","0.851;0.849;0.814;0.847",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","654,0","0","654","0/1","355,58","0.1404","413",null,"chr12:7501159:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1443"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CD163","chr12:7501159","CD163(D146V)",null,null,"topological domain (Extracellular ), domain (SRCR 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs905885266",-1,null,"FUNCTION: Acute phase-regulated receptor involved in clearance and endocytosis of hemoglobin/haptoglobin complexes by macrophages and may thereby protect tissues from free hemoglobin-mediated oxidative damage. May play a role in the uptake and recycling of iron, via endocytosis of hemoglobin/haptoglobin and subsequent breakdown of heme. Binds hemoglobin/haptoglobin complexes in a calcium-dependent and pH-dependent manner. Exhibits a higher affinity for complexes of hemoglobin and multimeric haptoglobin of HP*1F phenotype than for complexes of hemoglobin and dimeric haptoglobin of HP*1S phenotype. Induces a cascade of intracellular signals that involves tyrosine kinase-dependent calcium mobilization, inositol triphosphate production and secretion of IL6 and CSF1. Isoform 3 exhibits the higher capacity for ligand endocytosis and the more pronounced surface expression when expressed in cells.; ",{"$nulls":4},"p.Asp146Val","c.437A>T","MODERATE","146/1156",3,{"$nulls":5},"5","660","440","496","314","577","387","0","0","0","0.3359",{"$nulls":20},"4.057871","1.21","2.935;.;.;2.935","1","-4.84;-4.85;-5.34;-4.69","1.0;.;1.0;1.0","0.046;0.048;0.04;0.045","0.851;0.849;0.814;0.847",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","654,0","0","654","0/1","270,146","0.351","416",null,"chr12:7501159:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3599"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CDCP2","chr1:54152912","CDCP2(E4G)",{"$nulls":6},255,"PASS","Missense","rs1323528750",-1,{"$nulls":6},"p.Glu4Gly","c.11A>G","MODERATE","4/540",1,{"$nulls":5},"4","374","440","274","286","339","399","0","0","0","0.3083",{"$nulls":20},"1.743838",".;1.53",".;0","1",".;-1.04",".;0.001",".;0.112",".;0.046",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","285,133","0.3182","418",null,"chr1:54152912:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3007"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CHD6","chr20:41488518","CHD6(K589N)",null,null,"domain (Helicase ATP-binding ), region of interest (Required for DNA-dependent ATPase activity ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2. {ECO:0000269|PubMed:16314513, ECO:0000269|PubMed:28533432}.; ",{"$nulls":4},"p.Lys589Asn","c.1767G>C","MODERATE","589/2715",13,{"$nulls":5},"5","815","497","594","345","742","447","0","0","0","0.132",{"$nulls":20},"2.568535","-3.2;.","0.905;.","0.999913;1","-1.43;.","0.071;.","0.281;.","0.398;0.263",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the SNF2/RAD54 helicase protein family. The encoded protein contains two chromodomains, a helicase domain, and an ATPase domain. Several multi-subunit protein complexes remodel chromatin to allow patterns of cell type-specific gene expression, and the encoded protein is thought to be a core member of one or more of these chromatin remodeling complexes. The encoded protein may function as a transcriptional repressor and is involved in the cellular repression of influenza virus replication. [provided by RefSeq, Jul 2013].  ",null,null,"0/0","805,0","0","805","0/1","420,64","0.1322","484",null,"chr20:41488518:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1333"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CHD6","chr20:41488518","CHD6(K589N)",null,null,"domain (Helicase ATP-binding ), region of interest (Required for DNA-dependent ATPase activity ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2. {ECO:0000269|PubMed:16314513, ECO:0000269|PubMed:28533432}.; ",{"$nulls":4},"p.Lys589Asn","c.1767G>C","MODERATE","589/2715",13,{"$nulls":5},"5","815","575","594","395","741","501","0","0","0","0.2934",{"$nulls":20},"2.568535","-3.2;.","0.905;.","0.999913;1","-1.43;.","0.071;.","0.281;.","0.398;0.263",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the SNF2/RAD54 helicase protein family. The encoded protein contains two chromodomains, a helicase domain, and an ATPase domain. Several multi-subunit protein complexes remodel chromatin to allow patterns of cell type-specific gene expression, and the encoded protein is thought to be a core member of one or more of these chromatin remodeling complexes. The encoded protein may function as a transcriptional repressor and is involved in the cellular repression of influenza virus replication. [provided by RefSeq, Jul 2013].  ",null,null,"0/0","802,0","0","802","0/1","383,162","0.2972","545",null,"chr20:41488518:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2886"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CNKSR2","chrX:21426535","CNKSR2(E35*)",null,null,"domain (SAM ), helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Mental retardation, X-linked, syndromic, Houge type (MRXSHG) [MIM:301008]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXSHG is characterized by delayed development, intellectual disability, speech and language delay, and early-onset seizures. Carrier females may be mildly affected. {ECO:0000269|PubMed:25223753, ECO:0000269|PubMed:28098945}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May function as an adapter protein or regulator of Ras signaling pathways. {ECO:0000269|PubMed:14597674}.; ",{"$nulls":4},"p.Glu35*","c.103G>T","HIGH","35/1034",2,{"$nulls":5},"5","619","327","485","259","523","287","0","0","0","0.1463",{"$nulls":5},"(CNKSR2|ENSG00000149970|1|1.00)","(CNKSR2|ENSG00000149970|1|1.00)",{"$nulls":13},"6.331433",null,null,"1",{"$nulls":3},".;.;0.472;.;0.474;0.5;.;.;.;.;0.483;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4538788","0/0","617,0","0","617","0/1","275,46","0.1433","321",null,"chrX:21426535:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1429"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CNKSR2","chrX:21426535","CNKSR2(E35*)",null,null,"domain (SAM ), helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Mental retardation, X-linked, syndromic, Houge type (MRXSHG) [MIM:301008]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXSHG is characterized by delayed development, intellectual disability, speech and language delay, and early-onset seizures. Carrier females may be mildly affected. {ECO:0000269|PubMed:25223753, ECO:0000269|PubMed:28098945}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May function as an adapter protein or regulator of Ras signaling pathways. {ECO:0000269|PubMed:14597674}.; ",{"$nulls":4},"p.Glu35*","c.103G>T","HIGH","35/1034",2,{"$nulls":5},"5","619","395","485","293","528","337","0","0","0","0.2433",{"$nulls":5},"(CNKSR2|ENSG00000149970|1|1.00)","(CNKSR2|ENSG00000149970|1|1.00)",{"$nulls":13},"6.331433",null,null,"1",{"$nulls":3},".;.;0.472;.;0.474;0.5;.;.;.;.;0.483;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4538788","0/0","609,0","0","609","0/1","293,91","0.237","384",null,"chrX:21426535:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2423"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CSF1","chr1:109917293","CSF1(K76*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Aberrant expression of CSF1 or CSF1R can promote cancer cell proliferation, invasion and formation of metastases. Overexpression of CSF1 or CSF1R is observed in a significant percentage of breast, ovarian, prostate, and endometrial cancers.; DISEASE: Note=Aberrant expression of CSF1 or CSF1R may play a role in inflammatory diseases, such as rheumatoid arthritis, glomerulonephritis, atherosclerosis, and allograft rejection.; ","FUNCTION: Cytokine that plays an essential role in the regulation of survival, proliferation and differentiation of hematopoietic precursor cells, especially mononuclear phagocytes, such as macrophages and monocytes. Promotes the release of proinflammatory chemokines, and thereby plays an important role in innate immunity and in inflammatory processes. Plays an important role in the regulation of osteoclast proliferation and differentiation, the regulation of bone resorption, and is required for normal bone development. Required for normal male and female fertility. Promotes reorganization of the actin cytoskeleton, regulates formation of membrane ruffles, cell adhesion and cell migration. Plays a role in lipoprotein clearance. {ECO:0000269|PubMed:16337366, ECO:0000269|PubMed:19934330, ECO:0000269|PubMed:20504948, ECO:0000269|PubMed:20829061}.; ","gedi",{"$nulls":3},"p.Lys76*","c.226A>T","HIGH","76/554",4,{"$nulls":5},"5","447","296","392","242","343","221","0.0022","0.0022","0","0.1086",{"$nulls":5},"(CSF1|ENSG00000184371|1|1.00)","(CSF1|ENSG00000184371|1|1.00)",{"$nulls":13},"4.961215",null,null,"1",{"$nulls":3},".;.;.;0.897;.;0.897;0.905;0.897",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","442,1","0.0023","443","0/1","260,23","0.0813","283",null,"chr1:109917293:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0868"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CSMD2","chr1:33587160","CSMD2(L2289F)",null,null,"topological domain (Extracellular ), domain (CUB 13 ), splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu2289Phe","c.6865C>T","MODERATE","2289/3631",45,{"$nulls":5},"5","608","403","439","271","572","367","0","0","0","0.297",{"$nulls":20},"4.0928889999999996","1.7;.;.",".;2.985;.","0.999767","-3.39;.;.",".;0.997;.","0.004;.;.","0.783;0.703;0.823",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","604,0","0","604","0/1","271,120","0.3069","391",null,"chr1:33587160:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2989"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","CSMD2","chr1:33587160","CSMD2(L2289F)",null,null,"topological domain (Extracellular ), domain (CUB 13 ), splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu2289Phe","c.6865C>T","MODERATE","2289/3631",45,{"$nulls":5},"5","608","490","439","314","571","441","0","0","0","0.7347",{"$nulls":20},"4.0928889999999996","1.7;.;.",".;2.985;.","0.999767","-3.39;.;.",".;0.997;.","0.004;.;.","0.783;0.703;0.823",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","603,0","0","603","0/1","127,351","0.7343","478",null,"chr1:33587160:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7197"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","CYP2F1","chr19:41121987","CYP2F1(W226G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in the metabolism of various pneumotoxicants including naphthalene. Is able to dealkylate ethoxycoumarin, propoxycoumarin, and pentoxyresorufin but possesses no activity toward ethoxyresorufin and only trace dearylation activity toward benzyloxyresorufin. Bioactivates 3- methylindole (3MI) by dehydrogenation to the putative electrophile 3-methylene-indolenine. {ECO:0000269|PubMed:1974816}.; ",{"$nulls":4},"p.Trp226Gly","c.676T>G","MODERATE","226/491",6,{"$nulls":5},"4","384","284","438","269","440","28","0","0","0","0.2857",{"$nulls":20},"2.155349","-0.29","2.385","1","-4.69","0.82","0.003","0.401",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","377,0","0","377","0/1","224,38","0.145","262",null,"chr19:41121987:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1413"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","DDX58","chr9:32491332","DDX58(Q220H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Singleton-Merten syndrome 2 (SGMRT2) [MIM:616298]: A form of Singleton-Merten syndrome, an autosomal dominant disorder characterized by marked aortic calcification, dental anomalies, osteopenia, acro-osteolysis, and to a lesser extent glaucoma, psoriasis, muscle weakness, and joint laxity. Additional clinical manifestations include particular facial characteristics and abnormal joint and muscle ligaments. SGMRT2 is an atypical form characterized by variable expression of glaucoma, aortic calcification, and skeletal abnormalities, without dental anomalies. {ECO:0000269|PubMed:25620203}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include: 5'- triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity. Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK- related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration. {ECO:0000269|PubMed:15208624, ECO:0000269|PubMed:15708988, ECO:0000269|PubMed:16125763, ECO:0000269|PubMed:16127453, ECO:0000269|PubMed:16153868, ECO:0000269|PubMed:17190814, ECO:0000269|PubMed:18636086, ECO:0000269|PubMed:19122199, ECO:0000269|PubMed:19211564, ECO:0000269|PubMed:19576794, ECO:0000269|PubMed:19609254, ECO:0000269|PubMed:19631370, ECO:0000269|PubMed:21742966}.; ",{"$nulls":4},"p.Gln220His","c.660G>C","MODERATE","220/925",5,{"$nulls":5},"5","259","111","191","82","220","84","0","0","0","0.0714",{"$nulls":20},"1.9990489999999999","1.24",".;2.015","0.921399;0.90188;0.938513;0.90188;0.90188","-1.23;-1.39",".;0.974","0.018;0.077","0.096;0.17",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225380","0/0","259,0","0","259","0/1","103,7","0.0636","110",null,"chr9:32491332:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.061"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","DGCR14","chr22:19144616","DGCR14(S9A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser9Ala","c.25T>G","MODERATE","9/476",1,{"$nulls":5},"5","325","147","224","94","299","130","0","0","0","0.1462",{"$nulls":20},"0.144485","2.0",null,"1","-0.11",null,"0.904","0.088",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","317,0","0","317","0/1","120,22","0.1549","142",null,"chr22:19144616:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1596"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","DGCR14","chr22:19144616","DGCR14(S9A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser9Ala","c.25T>G","MODERATE","9/476",1,{"$nulls":5},"5","325","174","224","112","301","161","0","0","0","0.3975",{"$nulls":20},"0.144485","2.0",null,"1","-0.11",null,"0.904","0.088",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","317,0","0","317","0/1","88,69","0.4395","157",null,"chr22:19144616:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3929"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","DIS3L","chr15:66306832","DIS3L(N101I)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative cytoplasm-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. {ECO:0000269|PubMed:20531386, ECO:0000269|PubMed:20531389}.; ",{"$nulls":4},"p.Asn101Ile","c.302A>T","MODERATE","101/1054",3,{"$nulls":5},"5","450","323","356","239","387","292","0","0","0","0.3459",{"$nulls":20},"2.9655139999999998","1.72;.;1.71;.;.",".;.;2.755;.;.","0.999996;0.999996;1","-5.31;-7.28;-5.65;-5.17;-4.77",".;.;0.89;.;.","0.01;0.001;0.009;0.002;0.002","0.68;.;0.697;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","449,0","0","449","0/1","211,105","0.3323","316",null,"chr15:66306832:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3222"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","DLL3","chr19:39507277","DLL3(C444W)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spondylocostal dysostosis 1, autosomal recessive (SCDO1) [MIM:277300]: A condition of variable severity associated with vertebral and rib segmentation defects. The main skeletal malformations include fusion of vertebrae, hemivertebrae, fusion of certain ribs, and other rib malformations. Deformity of the chest and spine (severe scoliosis, kyphoscoliosis and lordosis) is a natural consequence of the malformation and leads to a dwarf- like appearance. As the thorax is small, infants frequently have respiratory insufficiency and repeated respiratory infections resulting in life-threatening complications in the first year of life. {ECO:0000269|PubMed:10742114}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Inhibits primary neurogenesis. May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm (By similarity). {ECO:0000250}.; ","level2",{"$nulls":3},"p.Cys444Trp","c.1332C>G","MODERATE","444/618",7,{"$nulls":5},"5","455","288","368","224","369","235","0","0","0","0.0936",{"$nulls":20},"4.57727","-5.72;-4.2;-2.63","4.59;.;4.59","1","-7.59;.;-7.59",".;.;0.998","0.001;.;0.001","0.831;.;0.835",{"$nulls":3},"Unknown",-1,"AR","Spondylocostal dysostosis 1, autosomal recessive","Musculoskeletal","kNOTCH",null,null,"CN032975","0/0","445,0","0","445","0/1","239,29","0.1082","268",null,"chr19:39507277:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1116"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","DLL3","chr19:39507277","DLL3(C444W)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spondylocostal dysostosis 1, autosomal recessive (SCDO1) [MIM:277300]: A condition of variable severity associated with vertebral and rib segmentation defects. The main skeletal malformations include fusion of vertebrae, hemivertebrae, fusion of certain ribs, and other rib malformations. Deformity of the chest and spine (severe scoliosis, kyphoscoliosis and lordosis) is a natural consequence of the malformation and leads to a dwarf- like appearance. As the thorax is small, infants frequently have respiratory insufficiency and repeated respiratory infections resulting in life-threatening complications in the first year of life. {ECO:0000269|PubMed:10742114}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Inhibits primary neurogenesis. May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm (By similarity). {ECO:0000250}.; ","level2",{"$nulls":3},"p.Cys444Trp","c.1332C>G","MODERATE","444/618",7,{"$nulls":5},"5","455","306","368","236","368","249","0","0","0","0.2811",{"$nulls":20},"4.57727","-5.72;-4.2;-2.63","4.59;.;4.59","1","-7.59;.;-7.59",".;.;0.998","0.001;.;0.001","0.831;.;0.835",{"$nulls":3},"Unknown",-1,"AR","Spondylocostal dysostosis 1, autosomal recessive","Musculoskeletal","kNOTCH",null,null,"CN032975","0/0","447,0","0","447","0/1","217,82","0.2742","299",null,"chr19:39507277:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2627"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","DNAH9","chr17:11629519","DNAH9(E485Q)",null,null,"region of interest (Stem ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.; ",{"$nulls":4},"p.Glu485Gln","c.1453G>C","MODERATE","485/4486",7,{"$nulls":5},"5","353","335","265","248","307","310","0","0","0","0.4581",{"$nulls":20},"3.091264","0.23","2.965;.","0.930685","-2.63;-2.66","0.99;.","0.043;0.038","0.476;0.464",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4749028","0/0","344,0","0","344","0/1","181,151","0.4548","332",null,"chr17:11629519:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4556"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","DOCK10","chr2:224804185","DOCK10(Q1399E)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-exchange factor (GEF) that activates CDC42 and RAC1 by exchanging bound GDP for free GTP. Essential for dendritic spine morphogenesis in Purkinje cells and in hippocampal neurons, via a CDC42-mediated pathway. Sustains B-cell lymphopoiesis in secondary lymphoid tissues and regulates FCER2/CD23 expression. {ECO:0000250|UniProtKB:Q8BZN6}.; ",{"$nulls":4},"p.Gln1399Glu","c.4194_4195delGCinsAG","MODERATE","1398/2186",39,{"$nulls":5},"4","545","312","391","210","462","258","0","0","0","0.0814",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","535,0","0","535","0/1","261,34","0.1153","295",null,"chr2:224804185:GC:CT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1095"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","DOCK10","chr2:224804185","DOCK10(Q1399E)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-exchange factor (GEF) that activates CDC42 and RAC1 by exchanging bound GDP for free GTP. Essential for dendritic spine morphogenesis in Purkinje cells and in hippocampal neurons, via a CDC42-mediated pathway. Sustains B-cell lymphopoiesis in secondary lymphoid tissues and regulates FCER2/CD23 expression. {ECO:0000250|UniProtKB:Q8BZN6}.; ",{"$nulls":4},"p.Gln1399Glu","c.4194_4195delGCinsAG","MODERATE","1398/2186",39,{"$nulls":5},"3",null,null,"391","228","462","278",null,null,"0","0.1763",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","535,0","0","535","0/1","253,69","0.2143","322",null,"chr2:224804185:GC:CT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1974"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","DYRK3","chr1:206635729","DYRK3(G9A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Dual-specificity protein kinase that promotes disassembly of several types of membraneless organelles during mitosis, such as stress granules, nuclear speckles and pericentriolar material (PubMed:29973724). Dual-specificity tyrosine-regulated kinases (DYRKs) autophosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues (PubMed:9748265, PubMed:29634919). Acts as a central dissolvase of membraneless organelles during the G2-to-M transition, after the nuclear- envelope breakdown: acts by mediating phosphorylation of multiple serine and threonine residues in unstructured domains of proteins, such as SRRM1 and PCM1 (PubMed:29973724). Does not mediate disassembly of all membraneless organelles: disassembly of P-body and nucleolus is not regulated by DYRK3 (PubMed:29973724). Dissolution of membraneless organelles at the onset of mitosis is also required to release mitotic regulators, such as ZNF207, from liquid-unmixed organelles where they are sequestered and keep them dissolved during mitosis (PubMed:29973724). Regulates mTORC1 by mediating the dissolution of stress granules: during stressful conditions, DYRK3 partitions from the cytosol to the stress granule, together with mTORC1 components, which prevents mTORC1 signaling (PubMed:23415227). When stress signals are gone, the kinase activity of DYRK3 is required for the dissolution of stress granule and mTORC1 relocation to the cytosol: acts by mediating the phosphorylation of the mTORC1 inhibitor AKT1S1, allowing full reactivation of mTORC1 signaling (PubMed:23415227). Also acts as a negative regulator of EPO-dependent erythropoiesis: may place an upper limit on red cell production during stress erythropoiesis (PubMed:10779429). Inhibits cell death due to cytokine withdrawal in hematopoietic progenitor cells (PubMed:10779429). Promotes cell survival upon genotoxic stress through phosphorylation of SIRT1: this in turn inhibits p53/TP53 activity and apoptosis (PubMed:20167603). {ECO:0000269|PubMed:10779429, ECO:0000269|PubMed:20167603, ECO:0000269|PubMed:23415227, ECO:0000269|PubMed:29634919, ECO:0000269|PubMed:29973724, ECO:0000269|PubMed:9748265}.; ",{"$nulls":4},"p.Gly9Ala","c.26G>C","MODERATE","9/588",1,{"$nulls":5},"5","133","89","95","72","121","74","0","0","0","0.0676",{"$nulls":20},"2.937017","-0.58","0.695","1;0.951136","0.18","0.088","0.156","0.312",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","132,0","0","132","0/1","79,7","0.0814","86",null,"chr1:206635729:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0694"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","EPN1","chr19:55695348","EPN1(L661F)",{"$nulls":6},255,"PASS","Missense","rs775123359",-1,null,"FUNCTION: Binds to membranes enriched in phosphatidylinositol 4,5- bisphosphate (PtdIns(4,5)P2). Modifies membrane curvature and facilitates the formation of clathrin-coated invaginations (By similarity). Regulates receptor-mediated endocytosis. {ECO:0000250, ECO:0000269|PubMed:10557078}.; ",{"$nulls":4},"p.Leu661Phe","c.1981C>T","MODERATE","661/662",11,{"$nulls":5},"4",null,null,"103","58","137","74",null,null,"0","0.2568",{"$nulls":20},"3.529865","1.76;1.68;1.48","0;.;.","0.993337;0.979763;0.993337;0.995977;1","-2.48;-2.31;-2.55","0.994;0.997;0.999","0.0","0.295;0.37;0.417",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene binds clathrin and is involved in the endocytosis of clathrin-coated vesicles. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011].",null,null,"0/0","146,0","0","150","0/1","68,20","0.2273","93",null,"chr19:55695348:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2414"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","EPN1","chr19:55695348","EPN1(L661F)",{"$nulls":6},255,"PASS","Missense","rs775123359",-1,null,"FUNCTION: Binds to membranes enriched in phosphatidylinositol 4,5- bisphosphate (PtdIns(4,5)P2). Modifies membrane curvature and facilitates the formation of clathrin-coated invaginations (By similarity). Regulates receptor-mediated endocytosis. {ECO:0000250, ECO:0000269|PubMed:10557078}.; ",{"$nulls":4},"p.Leu661Phe","c.1981C>T","MODERATE","661/662",11,{"$nulls":5},"4","150","70","103","48",null,null,"0","0",{"$nulls":22},"3.529865","1.76;1.68;1.48","0;.;.","0.993337;0.979763;0.993337;0.995977;1","-2.48;-2.31;-2.55","0.994;0.997;0.999","0.0","0.295;0.37;0.417",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene binds clathrin and is involved in the endocytosis of clathrin-coated vesicles. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011].",null,null,"0/0","143,0","0","143","0/1","31,30","0.4918","61",null,"chr19:55695348:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4792"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","EXO1","chr1:241881948","EXO1(S714R)",null,null,"region of interest (Interaction with MSH2 ), modified residue (Phosphoserine; by ATR), mutagenesis site (No rescue of HU-induced degradation and loss of HU-induced increase of phosphorylation. No rescue of HU-induced degradation; when associated with A-621. No rescue of HU-induced degradation; when associated with A-454. Loss of HU-sensitivity and resistance to HU-induced degradation; when associated with A-454 and A-621. EXO1(S714A))",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch- containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:10608837, ECO:0000269|PubMed:11809771, ECO:0000269|PubMed:11842105, ECO:0000269|PubMed:12414623, ECO:0000269|PubMed:12704184, ECO:0000269|PubMed:14636568, ECO:0000269|PubMed:14676842, ECO:0000269|PubMed:15225546, ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:16143102, ECO:0000269|PubMed:9685493}.; ","level2",{"$nulls":3},"p.Ser714Arg","c.2142T>A","MODERATE","714/846",12,{"$nulls":5},"5","218","166","142","104","176","142","0","0","0","0.0986",{"$nulls":20},"1.5109780000000002","1.24;1.24;1.12","0.69","0.829622","-1.97","0.183;0.183;0.33","0.024;0.024;0.027","0.192;0.192;0.194",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMISMATCH_REPAIR",{"$nulls":3},"0/0","212,0","0","212","0/1","145,17","0.1049","162",null,"chr1:241881948:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1154"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","EXO1","chr1:241881948","EXO1(S714R)",null,null,"region of interest (Interaction with MSH2 ), modified residue (Phosphoserine; by ATR), mutagenesis site (No rescue of HU-induced degradation and loss of HU-induced increase of phosphorylation. No rescue of HU-induced degradation; when associated with A-621. No rescue of HU-induced degradation; when associated with A-454. Loss of HU-sensitivity and resistance to HU-induced degradation; when associated with A-454 and A-621. EXO1(S714A))",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch- containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:10608837, ECO:0000269|PubMed:11809771, ECO:0000269|PubMed:11842105, ECO:0000269|PubMed:12414623, ECO:0000269|PubMed:12704184, ECO:0000269|PubMed:14636568, ECO:0000269|PubMed:14676842, ECO:0000269|PubMed:15225546, ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:16143102, ECO:0000269|PubMed:9685493}.; ","level2",{"$nulls":3},"p.Ser714Arg","c.2142T>A","MODERATE","714/846",12,{"$nulls":5},"5","218","205","142","132","177","171","0","0","0","0.152",{"$nulls":20},"1.5109780000000002","1.24;1.24;1.12","0.69","0.829622","-1.97","0.183;0.183;0.33","0.024;0.024;0.027","0.192;0.192;0.194",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMISMATCH_REPAIR",{"$nulls":3},"0/0","212,0","0","212","0/1","169,28","0.1421","197",null,"chr1:241881948:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1515"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","EXOC7","chr17:76097931","EXOC7(L169V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane. In adipocytes, plays a crucial role in targeting SLC2A4 vesicle to the plasma membrane in response to insulin, perhaps directing the vesicle to the precise site of fusion (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu169Val","c.505C>G","MODERATE","169/735",5,{"$nulls":5},"5","687","478","484","325","613","409","0","0","0","0.3276",{"$nulls":20},"2.285974",null,"1.1;1.1;1.1;.;.;.;1.1;1.1;.;.","0.999981;1;1;1;1;1","-0.05;.;0.08;.;.;-0.05;.;-0.05;0.02;0.13","0.955;0.006;0.004;0.083;0.083;.;0.006;0.077;.;.","1.0;.;0.946;.;.;0.961;.;1.0;1.0;1.0","0.684;0.721;0.679;0.729;0.729;0.741;0.725;0.713;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","677,0","0","677","0/1","314,155","0.3305","469",null,"chr17:76097931:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3169"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","F8","chrX:154929464","F8(K1442N)",null,null,"region of interest (B ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Hemophilia A (HEMA) [MIM:306700]: A disorder of blood coagulation characterized by a permanent tendency to hemorrhage. About 50% of patients have severe hemophilia resulting in frequent spontaneous bleeding into joints, muscles and internal organs. Less severe forms are characterized by bleeding after trauma or surgery. {ECO:0000269|PubMed:10215414, ECO:0000269|PubMed:10338101, ECO:0000269|PubMed:10404764, ECO:0000269|PubMed:10408784, ECO:0000269|PubMed:10554831, ECO:0000269|PubMed:10612839, ECO:0000269|PubMed:10691849, ECO:0000269|PubMed:10800171, ECO:0000269|PubMed:10886198, ECO:0000269|PubMed:10896236, ECO:0000269|PubMed:10910910, ECO:0000269|PubMed:10910913, ECO:0000269|PubMed:11298607, ECO:0000269|PubMed:11341489, ECO:0000269|PubMed:11410838, ECO:0000269|PubMed:11442643, ECO:0000269|PubMed:11442647, ECO:0000269|PubMed:11554935, ECO:0000269|PubMed:11748850, ECO:0000269|PubMed:11857744, ECO:0000269|PubMed:11858487, ECO:0000269|PubMed:12195713, ECO:0000269|PubMed:12199686, ECO:0000269|PubMed:12203998, ECO:0000269|PubMed:12325022, ECO:0000269|PubMed:12351418, ECO:0000269|PubMed:12406074, ECO:0000269|PubMed:12614369, ECO:0000269|PubMed:12871415, ECO:0000269|PubMed:12930394, ECO:0000269|PubMed:1301194, ECO:0000269|PubMed:1301932, ECO:0000269|PubMed:1301960, ECO:0000269|PubMed:1349567, ECO:0000269|PubMed:1356412, ECO:0000269|PubMed:15682412, ECO:0000269|PubMed:15810915, ECO:0000269|PubMed:1639429, ECO:0000269|PubMed:16805874, ECO:0000269|PubMed:18184865, ECO:0000269|PubMed:1851341, ECO:0000269|PubMed:1908096, ECO:0000269|PubMed:1908817, ECO:0000269|PubMed:1973901, ECO:0000269|PubMed:2104766, ECO:0000269|PubMed:2105106, ECO:0000269|PubMed:2105906, ECO:0000269|PubMed:2106480, ECO:0000269|PubMed:2107542, ECO:0000269|PubMed:21371196, ECO:0000269|PubMed:2495245, ECO:0000269|PubMed:2498882, ECO:0000269|PubMed:2499363, ECO:0000269|PubMed:2506948, ECO:0000269|PubMed:2510835, ECO:0000269|PubMed:25550078, ECO:0000269|PubMed:26278069, ECO:0000269|PubMed:2833855, ECO:0000269|PubMed:2835904, ECO:0000269|PubMed:3012775, ECO:0000269|PubMed:3122181, ECO:0000269|PubMed:7579394, ECO:0000269|PubMed:7759074, ECO:0000269|PubMed:7794769, ECO:0000269|PubMed:8322269, ECO:0000269|PubMed:8449505, ECO:0000269|PubMed:8639447, ECO:0000269|PubMed:8644728, ECO:0000269|PubMed:8759905, ECO:0000269|PubMed:9029040, ECO:0000269|PubMed:9326186, ECO:0000269|PubMed:9341862, ECO:0000269|PubMed:9450898, ECO:0000269|PubMed:9452104, ECO:0000269|PubMed:9569180, ECO:0000269|PubMed:9569189, ECO:0000269|PubMed:9603440, ECO:0000269|PubMed:9792405, ECO:0000269|PubMed:9829908, ECO:0000269|PubMed:9886318}. Note=The disease is caused by mutations affecting the gene represented in this entry. Of particular interest for the understanding of the function of F8 is the category of CRM (cross-reacting material) positive patients (approximately 5%) that have considerable amount of F8 in their plasma (at least 30% of normal), but the protein is non- functional; i.e. the F8 activity is much less than the plasma protein level. CRM-reduced is another category of patients in which the F8C antigen and activity are reduced to approximately the same level. Most mutations are CRM negative, and probably affect the folding and stability of the protein.; ","FUNCTION: Factor VIII, along with calcium and phospholipid, acts as a cofactor for F9/factor IXa when it converts F10/factor X to the activated form, factor Xa.; ",{"$nulls":4},"p.Lys1442Asn","c.4326G>C","MODERATE","1442/2351",14,{"$nulls":5},"4","2575","1654","2066","1332","2252","1451","0","0","0","0.1447",{"$nulls":20},"0.392028","-5.52","1.1","1","-0.18","0.097","0.068","0.106",{"$nulls":3},"Unknown",-1,"XL","Hemophilia A","Hematologic",{"$nulls":3},"C0019069","0/0","2395,0","0","2395","0/1","1326,225","0.1451","1551",null,"chrX:154929464:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1351"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","F8","chrX:154929464","F8(K1442N)",null,null,"region of interest (B ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Hemophilia A (HEMA) [MIM:306700]: A disorder of blood coagulation characterized by a permanent tendency to hemorrhage. About 50% of patients have severe hemophilia resulting in frequent spontaneous bleeding into joints, muscles and internal organs. Less severe forms are characterized by bleeding after trauma or surgery. {ECO:0000269|PubMed:10215414, ECO:0000269|PubMed:10338101, ECO:0000269|PubMed:10404764, ECO:0000269|PubMed:10408784, ECO:0000269|PubMed:10554831, ECO:0000269|PubMed:10612839, ECO:0000269|PubMed:10691849, ECO:0000269|PubMed:10800171, ECO:0000269|PubMed:10886198, ECO:0000269|PubMed:10896236, ECO:0000269|PubMed:10910910, ECO:0000269|PubMed:10910913, ECO:0000269|PubMed:11298607, ECO:0000269|PubMed:11341489, ECO:0000269|PubMed:11410838, ECO:0000269|PubMed:11442643, ECO:0000269|PubMed:11442647, ECO:0000269|PubMed:11554935, ECO:0000269|PubMed:11748850, ECO:0000269|PubMed:11857744, ECO:0000269|PubMed:11858487, ECO:0000269|PubMed:12195713, ECO:0000269|PubMed:12199686, ECO:0000269|PubMed:12203998, ECO:0000269|PubMed:12325022, ECO:0000269|PubMed:12351418, ECO:0000269|PubMed:12406074, ECO:0000269|PubMed:12614369, ECO:0000269|PubMed:12871415, ECO:0000269|PubMed:12930394, ECO:0000269|PubMed:1301194, ECO:0000269|PubMed:1301932, ECO:0000269|PubMed:1301960, ECO:0000269|PubMed:1349567, ECO:0000269|PubMed:1356412, ECO:0000269|PubMed:15682412, ECO:0000269|PubMed:15810915, ECO:0000269|PubMed:1639429, ECO:0000269|PubMed:16805874, ECO:0000269|PubMed:18184865, ECO:0000269|PubMed:1851341, ECO:0000269|PubMed:1908096, ECO:0000269|PubMed:1908817, ECO:0000269|PubMed:1973901, ECO:0000269|PubMed:2104766, ECO:0000269|PubMed:2105106, ECO:0000269|PubMed:2105906, ECO:0000269|PubMed:2106480, ECO:0000269|PubMed:2107542, ECO:0000269|PubMed:21371196, ECO:0000269|PubMed:2495245, ECO:0000269|PubMed:2498882, ECO:0000269|PubMed:2499363, ECO:0000269|PubMed:2506948, ECO:0000269|PubMed:2510835, ECO:0000269|PubMed:25550078, ECO:0000269|PubMed:26278069, ECO:0000269|PubMed:2833855, ECO:0000269|PubMed:2835904, ECO:0000269|PubMed:3012775, ECO:0000269|PubMed:3122181, ECO:0000269|PubMed:7579394, ECO:0000269|PubMed:7759074, ECO:0000269|PubMed:7794769, ECO:0000269|PubMed:8322269, ECO:0000269|PubMed:8449505, ECO:0000269|PubMed:8639447, ECO:0000269|PubMed:8644728, ECO:0000269|PubMed:8759905, ECO:0000269|PubMed:9029040, ECO:0000269|PubMed:9326186, ECO:0000269|PubMed:9341862, ECO:0000269|PubMed:9450898, ECO:0000269|PubMed:9452104, ECO:0000269|PubMed:9569180, ECO:0000269|PubMed:9569189, ECO:0000269|PubMed:9603440, ECO:0000269|PubMed:9792405, ECO:0000269|PubMed:9829908, ECO:0000269|PubMed:9886318}. Note=The disease is caused by mutations affecting the gene represented in this entry. Of particular interest for the understanding of the function of F8 is the category of CRM (cross-reacting material) positive patients (approximately 5%) that have considerable amount of F8 in their plasma (at least 30% of normal), but the protein is non- functional; i.e. the F8 activity is much less than the plasma protein level. CRM-reduced is another category of patients in which the F8C antigen and activity are reduced to approximately the same level. Most mutations are CRM negative, and probably affect the folding and stability of the protein.; ","FUNCTION: Factor VIII, along with calcium and phospholipid, acts as a cofactor for F9/factor IXa when it converts F10/factor X to the activated form, factor Xa.; ",{"$nulls":4},"p.Lys1442Asn","c.4326G>C","MODERATE","1442/2351",14,{"$nulls":5},"4","2575","2192","2066","1706","2250","1946","0","0","0","0.5144",{"$nulls":20},"0.392028","-5.52","1.1","1","-0.18","0.097","0.068","0.106",{"$nulls":3},"Unknown",-1,"XL","Hemophilia A","Hematologic",{"$nulls":3},"C0019069","0/0","2329,0","0","2329","0/1","967,997","0.5076","1964",null,"chrX:154929464:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.51"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","FGL2","chr7:77199562","FGL2(V78L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in physiologic lymphocyte functions at mucosal sites.; ",{"$nulls":4},"p.Val78Leu","c.232G>T","MODERATE","78/439",1,{"$nulls":5},"5","606","422","476","326","528","361","0","0","0","0.1025",{"$nulls":20},"2.436461","0.32;.","1.935;.","1;1;0.516749","-0.3;.","0.373;.","0.063;.","0.153;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","603,0","0","603","0/1","361,44","0.1086","405",null,"chr7:77199562:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1135"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","FGL2","chr7:77199562","FGL2(V78L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in physiologic lymphocyte functions at mucosal sites.; ",{"$nulls":4},"p.Val78Leu","c.232G>T","MODERATE","78/439",1,{"$nulls":5},"5","606","425","476","332","527","380","0","0","0","0.3237",{"$nulls":20},"2.436461","0.32;.","1.935;.","1;1;0.516749","-0.3;.","0.373;.","0.063;.","0.153;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","603,0","0","603","0/1","277,136","0.3293","413",null,"chr7:77199562:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3283"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","GARNL3","chr9:127264956","GARNL3(V27L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Val27Leu","c.79G>C","MODERATE","27/1013",1,{"$nulls":5},"4","867","558","640","385","748","469","0","0","0","0.1493",{"$nulls":20},"2.395477","1.79;0.76;.;0.92;-2.26;-2.29",".;.;.;.;.;1.5","0.957434","-0.5;-0.48;-1.2;-0.46;-0.37;-0.41",".;.;.;.;.;0.07","0.11;0.128;0.175;0.186;0.107;0.095",".;.;.;.;0.487;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","841,0","0","841","0/1","453,73","0.1388","526",null,"chr9:127264956:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1429"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","GARNL3","chr9:127264956","GARNL3(V27L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Val27Leu","c.79G>C","MODERATE","27/1013",1,{"$nulls":5},"4","867","358","640","253","747","310","0","0","0","0.4903",{"$nulls":20},"2.395477","1.79;0.76;.;0.92;-2.26;-2.29",".;.;.;.;.;1.5","0.957434","-0.5;-0.48;-1.2;-0.46;-0.37;-0.41",".;.;.;.;.;0.07","0.11;0.128;0.175;0.186;0.107;0.095",".;.;.;.;0.487;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","841,0","0","841","0/1","177,163","0.4794","340",null,"chr9:127264956:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4901"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","GJB7","chr6:87284650","GJB7(S88L)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: One gap junction consists of a cluster of closely packed pairs of transmembrane channels, the connexons, through which materials of low MW diffuse from one cell to a neighboring cell. {ECO:0000250, ECO:0000269|PubMed:12064583}.; ",{"$nulls":4},"p.Ser88Leu","c.263C>T","MODERATE","88/223",3,{"$nulls":5},"5","1006","677","792","509","858","588","0","0","0","0.3265",{"$nulls":20},"2.944158","-5.54","3.105;.","0.993571","-5.87;-6.0","1.0;.","0.001","0.507;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","981,0","0","981","0/1","427,217","0.337","644",null,"chr6:87284650:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3163"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","GPRASP2","chrX:102715675","GPRASP2(R269M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in regulation of a variety of G-protein coupled receptors. {ECO:0000269|PubMed:15086532}.; ",{"$nulls":4},"p.Arg269Met","c.806G>T","MODERATE","269/838",4,{"$nulls":5},"5","471","268","403","229","361","211","0","0","0","0.0616",{"$nulls":20},"0.947906","2.89","2.805","0.999238","-2.14","0.698","0.006","0.36;0.36;0.363",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4746975","0/0","471,0","0","471","0/1","255,15","0.0556","270",null,"chrX:102715675:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0611"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","GRHL2","chr8:101577442","GRHL2(N309T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Deafness, autosomal dominant, 28 (DFNA28) [MIM:608641]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA28 is characterized by mild to moderate hearing loss across most frequencies that progresses to severe loss in the higher frequencies by the fifth decade. {ECO:0000269|PubMed:12393799}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ectodermal dysplasia/short stature syndrome (ECTDS) [MIM:616029]: An autosomal recessive ectodermal dysplasia syndrome characterized by nail dystrophy and/or loss, oral mucosa and/or tongue pigmentation, abnormal dentition, keratoderma affecting the margins of the palms and soles, focal hyperkeratosis of the dorsal aspects of the hands and feet, and short stature. {ECO:0000269|PubMed:25152456}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Corneal dystrophy, posterior polymorphous, 4 (PPCD4) [MIM:618031]: A subtype of posterior corneal dystrophy, a disease characterized by alterations of Descemet membrane presenting as vesicles, opacities or band-like lesions on slit-lamp examination and specular microscopy. In severe cases, corneal endothelial failure may occur and corneal transplantation is required to restore vision. Secondary complications are common and include corneal edema, glaucoma, iris adherence to the cornea, and corectopia. PPCD4 transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:29499165}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor playing an important role in primary neurulation and in epithelial development (PubMed:29309642, PubMed:25152456). Binds directly to the consensus DNA sequence 5'-AACCGGTT-3' acting as an activator and repressor on distinct target genes (By similarity). During embryogenesis, plays unique and cooperative roles with GRHL3 in establishing distinct zones of primary neurulation. Essential for closure 3 (rostral end of the forebrain), functions cooperatively with GRHL3 in closure 2 (forebrain/midbrain boundary) and posterior neuropore closure (By similarity). Regulates epithelial morphogenesis acting as a target gene-associated transcriptional activator of apical junctional complex components. Up-regulates of CLDN3 and CLDN4, as well as of RAB25, which increases the CLDN4 protein and its localization at tight junctions (By similarity). Comprises an essential component of the transcriptional machinery that establishes appropriate expression levels of CLDN4 and CDH1 in different types of epithelia. Exhibits functional redundancy with GRHL3 in epidermal morphogenetic events and epidermal wound repair (By similarity). In lung, forms a regulatory loop with NKX2-1 that coordinates lung epithelial cell morphogenesis and differentiation (By similarity). In keratinocytes, plays a role in telomerase activation during cellular proliferation, regulates TERT expression by binding to TERT promoter region and inhibiting DNA methylation at the 5'-CpG island, possibly by interfering with DNMT1 enzyme activity (PubMed:19015635, PubMed:20938050). In addition, impairs keratinocyte differentiation and epidermal function by inhibiting the expression of genes clustered at the epidermal differentiation complex (EDC) as well as GRHL1 and GRHL3 through epigenetic mechanisms (PubMed:23254293). {ECO:0000250|UniProtKB:Q8K5C0, ECO:0000269|PubMed:19015635, ECO:0000269|PubMed:20938050, ECO:0000269|PubMed:20978075, ECO:0000269|PubMed:23254293, ECO:0000269|PubMed:25152456, ECO:0000269|PubMed:29309642, ECO:0000305|PubMed:12175488}.; ",{"$nulls":4},"p.Asn309Thr","c.926A>C","MODERATE","309/625",7,{"$nulls":5},"5","448","335","353","252","387","273","0","0","0","0.1282",{"$nulls":20},"2.006078","2.3;.;2.3","0.505;0.505;.","1","-1.59;.;-1.59","0.013;0.013;.","1.0;.;1.0","0.362;.;0.367",{"$nulls":3},"Unknown",-1,"AD/AR","Ectodermal dysplasia/short stature syndrome","Audiologic/Otolaryngologic; Dental; Dermatologic; Musculoskeletal",{"$nulls":3},"C1837640| C4747961| C4014987","0/0","449,0","0","449","0/1","271,43","0.1369","314",null,"chr8:101577442:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.127"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","GRHL2","chr8:101577442","GRHL2(N309T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Deafness, autosomal dominant, 28 (DFNA28) [MIM:608641]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA28 is characterized by mild to moderate hearing loss across most frequencies that progresses to severe loss in the higher frequencies by the fifth decade. {ECO:0000269|PubMed:12393799}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ectodermal dysplasia/short stature syndrome (ECTDS) [MIM:616029]: An autosomal recessive ectodermal dysplasia syndrome characterized by nail dystrophy and/or loss, oral mucosa and/or tongue pigmentation, abnormal dentition, keratoderma affecting the margins of the palms and soles, focal hyperkeratosis of the dorsal aspects of the hands and feet, and short stature. {ECO:0000269|PubMed:25152456}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Corneal dystrophy, posterior polymorphous, 4 (PPCD4) [MIM:618031]: A subtype of posterior corneal dystrophy, a disease characterized by alterations of Descemet membrane presenting as vesicles, opacities or band-like lesions on slit-lamp examination and specular microscopy. In severe cases, corneal endothelial failure may occur and corneal transplantation is required to restore vision. Secondary complications are common and include corneal edema, glaucoma, iris adherence to the cornea, and corectopia. PPCD4 transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:29499165}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor playing an important role in primary neurulation and in epithelial development (PubMed:29309642, PubMed:25152456). Binds directly to the consensus DNA sequence 5'-AACCGGTT-3' acting as an activator and repressor on distinct target genes (By similarity). During embryogenesis, plays unique and cooperative roles with GRHL3 in establishing distinct zones of primary neurulation. Essential for closure 3 (rostral end of the forebrain), functions cooperatively with GRHL3 in closure 2 (forebrain/midbrain boundary) and posterior neuropore closure (By similarity). Regulates epithelial morphogenesis acting as a target gene-associated transcriptional activator of apical junctional complex components. Up-regulates of CLDN3 and CLDN4, as well as of RAB25, which increases the CLDN4 protein and its localization at tight junctions (By similarity). Comprises an essential component of the transcriptional machinery that establishes appropriate expression levels of CLDN4 and CDH1 in different types of epithelia. Exhibits functional redundancy with GRHL3 in epidermal morphogenetic events and epidermal wound repair (By similarity). In lung, forms a regulatory loop with NKX2-1 that coordinates lung epithelial cell morphogenesis and differentiation (By similarity). In keratinocytes, plays a role in telomerase activation during cellular proliferation, regulates TERT expression by binding to TERT promoter region and inhibiting DNA methylation at the 5'-CpG island, possibly by interfering with DNMT1 enzyme activity (PubMed:19015635, PubMed:20938050). In addition, impairs keratinocyte differentiation and epidermal function by inhibiting the expression of genes clustered at the epidermal differentiation complex (EDC) as well as GRHL1 and GRHL3 through epigenetic mechanisms (PubMed:23254293). {ECO:0000250|UniProtKB:Q8K5C0, ECO:0000269|PubMed:19015635, ECO:0000269|PubMed:20938050, ECO:0000269|PubMed:20978075, ECO:0000269|PubMed:23254293, ECO:0000269|PubMed:25152456, ECO:0000269|PubMed:29309642, ECO:0000305|PubMed:12175488}.; ",{"$nulls":4},"p.Asn309Thr","c.926A>C","MODERATE","309/625",7,{"$nulls":5},"5","448","399","353","290","387","345","0","0","0","0.3101",{"$nulls":20},"2.006078","2.3;.;2.3","0.505;0.505;.","1","-1.59;.;-1.59","0.013;0.013;.","1.0;.;1.0","0.362;.;0.367",{"$nulls":3},"Unknown",-1,"AD/AR","Ectodermal dysplasia/short stature syndrome","Audiologic/Otolaryngologic; Dental; Dermatologic; Musculoskeletal",{"$nulls":3},"C1837640| C4747961| C4014987","0/0","440,0","0","440","0/1","273,113","0.2927","386",null,"chr8:101577442:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2655"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","GRM3","chr7:86786621","GRM3(R277C)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: G-protein coupled receptor for glutamate. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Signaling inhibits adenylate cyclase activity. {ECO:0000269|PubMed:8840013}.; ",{"$nulls":5},"c.829C>T","HIGH",null,3,2,{"$nulls":4},"3","1534","892",{"$nulls":4},"0.0007","0.0007",{"$nulls":22},"4.005062","-1.76","2.65;.;2.65","1","-5.31;-6.52;-6.22","0.976;.;.","0.012;0.025;0.018","0.784;.;0.795",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1498,1","0.0007","1499","0/1","787,84","0.0964","871",null,"chr7:86786621:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","HDGF","chr1:156744171","HDGF(L177V)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Heparin-binding protein, with mitogenic activity for fibroblasts. Acts as a transcriptional repressor. {ECO:0000269|PubMed:17974029}.; ",{"$nulls":4},"p.Leu177Val","c.529T>G","MODERATE","177/256",4,{"$nulls":5},"5","209","258","172","208","150","192","0","0","0","0.2188",{"$nulls":20},"0.124352","1.93;1.93;1.51;1.51","1.59;1.59;.;.","0.999998;0.999999;0.999999;0.999998;0.999999","0.02;0.02;0.16;0.16","0.0;0.0;.;.","1.0;1.0;0.779;0.964","0.108;0.109;0.059;0.062",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","205,0","0","205","0/1","201,48","0.1928","249",null,"chr1:156744171:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2115"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","HIST1H2BF","chr6:26199826","HIST1H2BF(I90F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.; ",{"$nulls":4},"p.Ile90Phe","c.268A>T","MODERATE","90/126",1,{"$nulls":5},"4","1510","1050","1254","831","676","374","0","0","0","0.2326",{"$nulls":20},"3.770406","-1.03",null,"0.972066","-3.79",null,null,"0.938",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1482,1","0.0007","1483","0/1","886,132","0.1297","1018",null,"chr6:26199826:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1215"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","HIST2H3D","chr1:149813665","HIST2H3D(Q6L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.; ",{"$nulls":4},"p.Gln6Leu","c.17A>T","MODERATE","6/136",1,{"$nulls":5},"4",null,null,"712","531","878","197",null,null,"0","0.198",{"$nulls":20},"2.965033","0.82",null,"0.999538","-5.04",null,null,"0.796",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","895,0","0","895","0/1","571,89","0.1348","660",null,"chr1:149813665:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1262"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ITGB4","chr17:75748981","ITGB4(S1084R)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Epidermolysis bullosa letalis, with pyloric atresia (EB- PA) [MIM:226730]: An autosomal recessive, frequently lethal, epidermolysis bullosa with variable involvement of skin, nails, mucosa, and with variable effects on the digestive system. It is characterized by mucocutaneous fragility, aplasia cutis congenita, and gastrointestinal atresia, which most commonly affects the pylorus. Pyloric atresia is a primary manifestation rather than a scarring process secondary to epidermolysis bullosa. {ECO:0000269|PubMed:10873890, ECO:0000269|PubMed:11251584, ECO:0000269|PubMed:11328943, ECO:0000269|PubMed:9422533, ECO:0000269|PubMed:9546354, ECO:0000269|PubMed:9792864, ECO:0000269|PubMed:9892956}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Generalized atrophic benign epidermolysis bullosa (GABEB) [MIM:226650]: A non-lethal, adult form of junctional epidermolysis bullosa characterized by life-long blistering of the skin, associated with hair and tooth abnormalities. {ECO:0000269|PubMed:10792571}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa simplex, Weber-Cockayne type (WC- EBS) [MIM:131800]: A form of intraepidermal epidermolysis bullosa characterized by blistering limited to palmar and plantar areas of the skin. {ECO:0000269|PubMed:12485428}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Integrin alpha-6/beta-4 is a receptor for laminin. Plays a critical structural role in the hemidesmosome of epithelial cells. Is required for the regulation of keratinocyte polarity and motility. ITGA6:ITGB4 binds to NRG1 (via EGF domain) and this binding is essential for NRG1-ERBB signaling (PubMed:20682778). ITGA6:ITGB4 binds to IGF1 and this binding is essential for IGF1 signaling (PubMed:22351760). ITGA6:ITGB4 binds to IGF2 and this binding is essential for IGF2 signaling (PubMed:28873464). {ECO:0000269|PubMed:12482924, ECO:0000269|PubMed:19403692, ECO:0000269|PubMed:20682778, ECO:0000269|PubMed:22351760, ECO:0000269|PubMed:28873464}.; ",{"$nulls":5},"c.3252C>G","HIGH",null,27,{"$nulls":5},"5","578","338","446","266","497","281","0","0","0","0.3025",{"$nulls":20},"3.080225","1.48","2.34","0.999375",".;-1.92;.;-1.92",".;0.785;.;0.677",".;0.004;.;0.004","0.56;0.565;0.561;0.56",{"$nulls":3},"Unknown",-1,"AD/AR","Epidermolysis bullosa, junctional, with pyloric atresia; Epidermolysis bullosa, junctional, non-Herlitz type; Epidermolysis bullosa simplex, Weber-Cockayne type ","Dermatologic; Gastrointestinal; Renal",{"$nulls":3},"C0268374| C0080333| C1856934","0/0","565,0","0","565","0/1","222,102","0.3148","324",null,"chr17:75748981:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.297"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ITGB4","chr17:75748981","ITGB4(S1084R)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Epidermolysis bullosa letalis, with pyloric atresia (EB- PA) [MIM:226730]: An autosomal recessive, frequently lethal, epidermolysis bullosa with variable involvement of skin, nails, mucosa, and with variable effects on the digestive system. It is characterized by mucocutaneous fragility, aplasia cutis congenita, and gastrointestinal atresia, which most commonly affects the pylorus. Pyloric atresia is a primary manifestation rather than a scarring process secondary to epidermolysis bullosa. {ECO:0000269|PubMed:10873890, ECO:0000269|PubMed:11251584, ECO:0000269|PubMed:11328943, ECO:0000269|PubMed:9422533, ECO:0000269|PubMed:9546354, ECO:0000269|PubMed:9792864, ECO:0000269|PubMed:9892956}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Generalized atrophic benign epidermolysis bullosa (GABEB) [MIM:226650]: A non-lethal, adult form of junctional epidermolysis bullosa characterized by life-long blistering of the skin, associated with hair and tooth abnormalities. {ECO:0000269|PubMed:10792571}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epidermolysis bullosa simplex, Weber-Cockayne type (WC- EBS) [MIM:131800]: A form of intraepidermal epidermolysis bullosa characterized by blistering limited to palmar and plantar areas of the skin. {ECO:0000269|PubMed:12485428}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Integrin alpha-6/beta-4 is a receptor for laminin. Plays a critical structural role in the hemidesmosome of epithelial cells. Is required for the regulation of keratinocyte polarity and motility. ITGA6:ITGB4 binds to NRG1 (via EGF domain) and this binding is essential for NRG1-ERBB signaling (PubMed:20682778). ITGA6:ITGB4 binds to IGF1 and this binding is essential for IGF1 signaling (PubMed:22351760). ITGA6:ITGB4 binds to IGF2 and this binding is essential for IGF2 signaling (PubMed:28873464). {ECO:0000269|PubMed:12482924, ECO:0000269|PubMed:19403692, ECO:0000269|PubMed:20682778, ECO:0000269|PubMed:22351760, ECO:0000269|PubMed:28873464}.; ",{"$nulls":5},"c.3252C>G","HIGH",null,27,{"$nulls":5},"5","578","412","446","308","498","351","0","0","0","0.2336",{"$nulls":20},"3.080225","1.48","2.34","0.999375",".;-1.92;.;-1.92",".;0.785;.;0.677",".;0.004;.;0.004","0.56;0.565;0.561;0.56",{"$nulls":3},"Unknown",-1,"AD/AR","Epidermolysis bullosa, junctional, with pyloric atresia; Epidermolysis bullosa, junctional, non-Herlitz type; Epidermolysis bullosa simplex, Weber-Cockayne type ","Dermatologic; Gastrointestinal; Renal",{"$nulls":3},"C0268374| C0080333| C1856934","0/0","566,0","0","566","0/1","287,108","0.2734","395",null,"chr17:75748981:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2597"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","KIF26B","chr1:245688256","KIF26B(F1758Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Essential for embryonic kidney development. Plays an important role in the compact adhesion between mesenchymal cells adjacent to the ureteric buds, possibly by interacting with MYH10. This could lead to the establishment of the basolateral integrity of the mesenchyme and the polarized expression of ITGA8, which maintains the GDNF expression required for further ureteric bud attraction. Although it seems to lack ATPase activity it is constitutively associated with microtubules (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Phe1758Tyr","c.5273_5274delTCinsAT","MODERATE","1758/2108",12,{"$nulls":5},"4","705","606","550","453","571","498","0","0","0","0.0964",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","687,0","0","687","0/1","522,55","0.0953","577",null,"chr1:245688256:TC:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0993"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","LRMP","chr12:25108043","LRMP(G1450R)",{"$nulls":6},255,"PASS","Missense","rs756832239",6e-05,null,"FUNCTION: Plays a role in the delivery of peptides to major histocompatibility complex (MHC) class I molecules; this occurs in a transporter associated with antigen processing (TAP)-independent manner. May play a role in taste signal transduction via ITPR3. May play a role during fertilization in pronucleus congression and fusion.; ",{"$nulls":4},"p.Gly1450Arg","c.4348G>C","MODERATE","1450/1454",39,{"$nulls":5},"4","310","218","233","161",null,null,"0","0",{"$nulls":22},"3.4732",".;2.36;2.36;2.36;2.36",null,"0.999999",".;-4.14;-4.14;-4.14;-4.14",null,".;0.001;0.002;0.001;0.001",".;0.392;0.267;0.436;0.391",{"$nulls":3},"ExAC_NFE_AF",6e-05,{"$nulls":4},"The protein encode dby this gene is expressed in a developmentally regulated manner in lymphoid cell lines and tissues. The protein is localized to the cytoplasmic face of the endoplasmic reticulum. [provided by RefSeq, Jul 2008].",null,null,"0/0","302,0","0","302","0/1","207,13","0.0591","220",null,"chr12:25108043:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0559"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","LRP1","chr12:57169172","LRP1(G1010S)",null,null,"topological domain (Extracellular ), domain (LDL-receptor class A 6 ), disulfide bond , splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense","rs773782629",1.2190000000000001E-4,"DISEASE: Keratosis pilaris atrophicans (KPA) [MIM:604093]: A group of rare genodermatoses characterized by keratotic follicular papules, variable degrees of inflammation, and secondary atrophic scarring. Most cases are associated with an atopic diathesis and keratosis pilaris on the extensor extremities. KPA is comprised of three distinct clinical subtypes: keratosis pilaris atrophicans faciei, atrophoderma vermiculatum, and keratosis follicularis spinulosa decalvans. Affected individuals may present with features overlapping the 3 subtypes. {ECO:0000269|PubMed:26142438}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Endocytic receptor involved in endocytosis and in phagocytosis of apoptotic cells. Required for early embryonic development. Involved in cellular lipid homeostasis. Involved in the plasma clearance of chylomicron remnants and activated LRPAP1 (alpha 2-macroglobulin), as well as the local metabolism of complexes between plasminogen activators and their endogenous inhibitors. May modulate cellular events, such as APP metabolism, kinase-dependent intracellular signaling, neuronal calcium signaling as well as neurotransmission (PubMed:11907044, PubMed:12888553, PubMed:12713657). Acts as an alpha-2- macroglobulin receptor (PubMed:26142438). {ECO:0000269|PubMed:11907044, ECO:0000269|PubMed:12713657, ECO:0000269|PubMed:12888553, ECO:0000269|PubMed:26142438}.; ",{"$nulls":4},"p.Gly1010Ser","c.3028G>A","MODERATE","1010/4544",20,{"$nulls":5},"5","1085","560","876","433","861","460","0","0","0","0.1478",{"$nulls":20},"4.225002","-3.61","1.07","0.999994","-2.78","1.0","0.113","0.46",{"$nulls":3},"ExAC_SAS_AF",1.2190000000000001E-4,"AD","Schizophrenia","Neurologic",{"$nulls":3},"C0263383","0/0","1069,0","0","1069","0/1","453,91","0.1673","544",null,"chr12:57169172:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1663"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","LRP1","chr12:57169172","LRP1(G1010S)",null,null,"topological domain (Extracellular ), domain (LDL-receptor class A 6 ), disulfide bond , splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Missense","rs773782629",1.2190000000000001E-4,"DISEASE: Keratosis pilaris atrophicans (KPA) [MIM:604093]: A group of rare genodermatoses characterized by keratotic follicular papules, variable degrees of inflammation, and secondary atrophic scarring. Most cases are associated with an atopic diathesis and keratosis pilaris on the extensor extremities. KPA is comprised of three distinct clinical subtypes: keratosis pilaris atrophicans faciei, atrophoderma vermiculatum, and keratosis follicularis spinulosa decalvans. Affected individuals may present with features overlapping the 3 subtypes. {ECO:0000269|PubMed:26142438}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Endocytic receptor involved in endocytosis and in phagocytosis of apoptotic cells. Required for early embryonic development. Involved in cellular lipid homeostasis. Involved in the plasma clearance of chylomicron remnants and activated LRPAP1 (alpha 2-macroglobulin), as well as the local metabolism of complexes between plasminogen activators and their endogenous inhibitors. May modulate cellular events, such as APP metabolism, kinase-dependent intracellular signaling, neuronal calcium signaling as well as neurotransmission (PubMed:11907044, PubMed:12888553, PubMed:12713657). Acts as an alpha-2- macroglobulin receptor (PubMed:26142438). {ECO:0000269|PubMed:11907044, ECO:0000269|PubMed:12713657, ECO:0000269|PubMed:12888553, ECO:0000269|PubMed:26142438}.; ",{"$nulls":4},"p.Gly1010Ser","c.3028G>A","MODERATE","1010/4544",20,{"$nulls":5},"5","1085","747","876","594","865","590","0","0","0","0.2661",{"$nulls":20},"4.225002","-3.61","1.07","0.999994","-2.78","1.0","0.113","0.46",{"$nulls":3},"ExAC_SAS_AF",1.2190000000000001E-4,"AD","Schizophrenia","Neurologic",{"$nulls":3},"C0263383","0/0","1068,1","0.0009","1069","0/1","521,199","0.2764","720",null,"chr12:57169172:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2727"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","LRP1B","chr2:140335786","LRP1B(N3982T)",null,null,"topological domain (Extracellular ), repeat (LDL-receptor class B 32 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential cell surface proteins that bind and internalize ligands in the process of receptor-mediated endocytosis.; ","gedi|foundationOne",{"$nulls":3},"p.Asn3982Thr","c.11945A>C","MODERATE","3982/4599",78,{"$nulls":5},"3","433","272","306","187",null,null,"0","0",{"$nulls":22},"4.027813","-3.21","2.535","0.999205","-2.93","0.993","0.007","0.809",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","421,0","0","421","0/1","252,14","0.0526","266",null,"chr2:140335786:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","MACROD2","chr20:15499786","MACROD2(E195V)",null,null,"domain (Macro ), splice variant (In isoform 6. ), splice variant (In isoform 4 and isoform 5. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Removes ADP-ribose from glutamate residues in proteins bearing a single ADP-ribose moiety. Inactive towards proteins bearing poly-ADP-ribose. Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. {ECO:0000269|PubMed:21257746, ECO:0000269|PubMed:23474712}.; ",{"$nulls":4},"p.Glu195Val","c.584A>T","MODERATE","195/425",8,{"$nulls":5},"5","602","404","457","299","532","362","0","0","0","0.2459",{"$nulls":20},"3.400599","1.74;.","2.165;.","0.990179;0.990179;1","-5.32;.","0.999;.","0.071;.","0.795;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","589,0","0","589","0/1","290,97","0.2506","387",null,"chr20:15499786:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2475"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","MCRS1","chr12:49564843","MCRS1(G127A)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Modulates the transcription repressor activity of DAXX by recruiting it to the nucleolus (PubMed:11948183). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (PubMed:20018852). Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. May also be an inhibitor of TERT telomerase activity (PubMed:15044100). Binds to G-quadruplex structures in mRNA (PubMed:16571602). Binds to RNA homopolymer poly(G) and poly(U) (PubMed:16571602). {ECO:0000269|PubMed:11948183, ECO:0000269|PubMed:15044100, ECO:0000269|PubMed:16571602, ECO:0000269|PubMed:20018852}.; ",{"$nulls":4},"p.Gly127Ala","c.380G>C","MODERATE","127/475",4,{"$nulls":5},"5","410","208","302","157","364","182","0","0","0","0.1538",{"$nulls":20},"1.9659200000000001",null,"1.1;1.1;.;.;.;.;.","1;0.772409;0.772409;0.900864","0.54;0.54;0.54;0.54;0.64;0.57;-0.41","0.0;0.0;0.0;0.0;.;.;.","0.234;0.234;0.266;0.479;0.635;0.583;0.097","0.134;0.134;0.129;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","405,0","0","405","0/1","164,39","0.1921","203",null,"chr12:49564843:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1847"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","MCRS1","chr12:49564843","MCRS1(G127A)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Modulates the transcription repressor activity of DAXX by recruiting it to the nucleolus (PubMed:11948183). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (PubMed:20018852). Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. May also be an inhibitor of TERT telomerase activity (PubMed:15044100). Binds to G-quadruplex structures in mRNA (PubMed:16571602). Binds to RNA homopolymer poly(G) and poly(U) (PubMed:16571602). {ECO:0000269|PubMed:11948183, ECO:0000269|PubMed:15044100, ECO:0000269|PubMed:16571602, ECO:0000269|PubMed:20018852}.; ",{"$nulls":4},"p.Gly127Ala","c.380G>C","MODERATE","127/475",4,{"$nulls":5},"5","410","301","302","204","365","271","0","0","0","0.2509",{"$nulls":20},"1.9659200000000001",null,"1.1;1.1;.;.;.;.;.","1;0.772409;0.772409;0.900864","0.54;0.54;0.54;0.54;0.64;0.57;-0.41","0.0;0.0;0.0;0.0;.;.;.","0.234;0.234;0.266;0.479;0.635;0.583;0.097","0.134;0.134;0.129;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","405,0","0","405","0/1","214,69","0.2438","283",null,"chr12:49564843:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2549"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","MMP11","chr22:23780588","MMP11(W163C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play an important role in the progression of epithelial malignancies.; ",{"$nulls":4},"p.Trp163Cys","c.489G>C","MODERATE","163/488",4,{"$nulls":5},"4","1266","696","974","518","1126","600","0","0","0","0.13",{"$nulls":20},"4.224201","2.07","2.045","1","-5.98","1.0","0.001","0.724",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1246,1","0.0008","1247","0/1","592,89","0.1307","681",null,"chr22:23780588:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1429"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","MMP11","chr22:23780588","MMP11(W163C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play an important role in the progression of epithelial malignancies.; ",{"$nulls":4},"p.Trp163Cys","c.489G>C","MODERATE","163/488",4,{"$nulls":5},"4","1266","693","974","487","1126","588","0","0","0","0.4796",{"$nulls":20},"4.224201","2.07","2.045","1","-5.98","1.0","0.001","0.724",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1250,1","0.0008","1251","0/1","341,333","0.4941","674",null,"chr22:23780588:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4846"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","MTMR12","chr5:32229872","MTMR12(K717T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularin intracellular location. {ECO:0000269|PubMed:11504939, ECO:0000269|PubMed:12847286}.; ",{"$nulls":4},"p.Lys717Thr","c.2150A>C","MODERATE","717/747",16,{"$nulls":5},"4","804","363","641","295","691","319","0.0012","0.0012","0","0.4639",{"$nulls":20},"3.745087","-4.04;-3.58;-3.54",".;0.895;.","0.982184;0.982184;0.985632","-1.42;-1.68;-1.35","0.999;0.998;0.995","0.106;0.004;0.02","0.374;0.419;0.508",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Phosphatidylinositide 3-kinase-derived membrane-anchored phosphatidylinositides, such as phosphatidylinositol 3-phosphate (PtdIns(3)P), regulate diverse cellular processes. The protein encoded by this gene functions as an adaptor subunit in a complex with an active PtdIns(3)P 3-phosphatase. Alternatively spliced transcript variants have been identified, but their biological validity has not been determined. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","790,1","0.0013","791","0/1","200,157","0.4398","357",null,"chr5:32229872:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4576"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","MXRA5","chrX:3317617","MXRA5(V2022I)",{"$nulls":6},255,"PASS","Missense","rs140532419",2.346805736636245E-3,"DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. {ECO:0000269|PubMed:22696596}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; ","FUNCTION: In kidney, has anti-inflammatory and anti-fibrotic properties by limiting the induction of chemokines, fibronectin and collagen expression in response to TGB1 and pro-inflammatory stimuli. {ECO:0000269|PubMed:27599751}.; ","gedi",{"$nulls":3},"p.Val2022Ile","c.6064G>A","MODERATE","2022/2828",6,5,{"$nulls":4},"4","1080","696","852","532","922","584","0.0009","0.0009","0","0.1182",{"$nulls":20},"2.410571","-0.22","0.605","0.990095","0.04","0.903","0.331","0.137",{"$nulls":3},"ESP6500_AA_AF",2.346805736636245E-3,{"$nulls":7},"0/0","1063,3","0.0028","1066","0/1","596,86","0.1261","682",null,"chrX:3317617:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1316"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","MXRA5","chrX:3317617","MXRA5(V2022I)",{"$nulls":6},255,"PASS","Missense","rs140532419",2.346805736636245E-3,"DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. {ECO:0000269|PubMed:22696596}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; ","FUNCTION: In kidney, has anti-inflammatory and anti-fibrotic properties by limiting the induction of chemokines, fibronectin and collagen expression in response to TGB1 and pro-inflammatory stimuli. {ECO:0000269|PubMed:27599751}.; ","gedi",{"$nulls":3},"p.Val2022Ile","c.6064G>A","MODERATE","2022/2828",6,5,{"$nulls":4},"4","1080","847","852","635","924","721","0.0009","0.0009","0","0.276",{"$nulls":20},"2.410571","-0.22","0.605","0.990095","0.04","0.903","0.331","0.137",{"$nulls":3},"ESP6500_AA_AF",2.346805736636245E-3,{"$nulls":7},"0/0","1061,3","0.0028","1064","0/1","598,228","0.276","826",null,"chrX:3317617:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2756"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","NOP56","chr20:2652905","NOP56(E23Q)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia 36 (SCA36) [MIM:614153]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA36 is characterized by complicated clinical features, with ataxia as the first symptom, followed by characteristic late-onset involvement of the motor neuron system. Ataxic symptoms, such as gait and truncal instability, ataxic dysarthria, and uncoordinated limbs, start in late forties to fifties. Characteristically, affected individuals exhibit tongue atrophy with fasciculation. Progression of motor neuron involvement is typically limited to the tongue and main proximal skeletal muscles in both upper and lower extremities. {ECO:0000269|PubMed:21683323}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by large hexanucleotide CGCCTG repeat expansions within intron 1. These expansions induce RNA foci and sequester the RNA-binding protein SRSF2. In addition, the transcription of MIR1292, a microRNA gene located just 19 bp 3' of the GGCCTG repeat, is significantly decreased.; ","FUNCTION: Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs. {ECO:0000269|PubMed:12777385, ECO:0000269|PubMed:15574333}.; ",{"$nulls":4},"p.Glu23Gln","c.67G>C","MODERATE","23/594",2,{"$nulls":5},"5","590","407","414","276","499","304","0","0","0","0.0888",{"$nulls":20},"4.68903","0.25;0.83","3.42;.","1","-2.65;-2.76","0.998;.","0.083;0.014","0.41;.",{"$nulls":3},"Unknown",-1,"AD ","Spinocerebellar ataxia 36","Neurologic",null,"Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is similar in sequence to Nop56p and is also found in the nucleolus. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jan 2009].",null,"C3472711","0/0","582,0","0","582","0/1","338,56","0.1421","394",null,"chr20:2652905:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1341"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","NOP56","chr20:2652905","NOP56(E23Q)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia 36 (SCA36) [MIM:614153]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA36 is characterized by complicated clinical features, with ataxia as the first symptom, followed by characteristic late-onset involvement of the motor neuron system. Ataxic symptoms, such as gait and truncal instability, ataxic dysarthria, and uncoordinated limbs, start in late forties to fifties. Characteristically, affected individuals exhibit tongue atrophy with fasciculation. Progression of motor neuron involvement is typically limited to the tongue and main proximal skeletal muscles in both upper and lower extremities. {ECO:0000269|PubMed:21683323}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by large hexanucleotide CGCCTG repeat expansions within intron 1. These expansions induce RNA foci and sequester the RNA-binding protein SRSF2. In addition, the transcription of MIR1292, a microRNA gene located just 19 bp 3' of the GGCCTG repeat, is significantly decreased.; ","FUNCTION: Involved in the early to middle stages of 60S ribosomal subunit biogenesis. Core component of box C/D small nucleolar ribonucleoprotein (snoRNP) particles. Required for the biogenesis of box C/D snoRNAs such U3, U8 and U14 snoRNAs. {ECO:0000269|PubMed:12777385, ECO:0000269|PubMed:15574333}.; ",{"$nulls":4},"p.Glu23Gln","c.67G>C","MODERATE","23/594",2,{"$nulls":5},"5","590","417","414","284","499","294","0","0","0","0.2279",{"$nulls":20},"4.68903","0.25;0.83","3.42;.","1","-2.65;-2.76","0.998;.","0.083;0.014","0.41;.",{"$nulls":3},"Unknown",-1,"AD ","Spinocerebellar ataxia 36","Neurologic",null,"Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is similar in sequence to Nop56p and is also found in the nucleolus. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jan 2009].",null,"C3472711","0/0","582,0","0","582","0/1","266,145","0.3528","411",null,"chr20:2652905:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3521"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","NOTCH2","chr1:119923840","NOTCH2(L1552F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Alagille syndrome 2 (ALGS2) [MIM:610205]: A form of Alagille syndrome, an autosomal dominant multisystem disorder. It is clinically defined by hepatic bile duct paucity and cholestasis in association with cardiac, skeletal, and ophthalmologic manifestations. There are characteristic facial features and less frequent clinical involvement of the renal and vascular systems. {ECO:0000269|PubMed:16773578}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hajdu-Cheney syndrome (HJCYS) [MIM:102500]: A rare, autosomal dominant skeletal disorder characterized by the association of facial anomalies, acro-osteolysis, general osteoporosis, insufficient ossification of the skull, and periodontal disease (premature loss of permanent teeth). Other features include cleft palate, congenital heart defects, polycystic kidneys, orthopedic problems and anomalies of the genitalia, intestines and eyes. {ECO:0000269|PubMed:21378985, ECO:0000269|PubMed:21378989, ECO:0000269|PubMed:21681853, ECO:0000269|PubMed:21712856, ECO:0000269|PubMed:21793104, ECO:0000269|PubMed:23389697, ECO:0000269|PubMed:29149593}. Note=The disease is caused by mutations affecting the gene represented in this entry. NOTCH2 nonsense and frameshift mutations associated with Hajdu-Cheney syndrome cluster to the last coding exon of the gene. Mutant mRNA products escape nonsense-mediated decay and the resulting truncated NOTCH2 proteins act in a gain-of-function manner (PubMed:21378989). The pathological mechanism at cellular level involves disruption of a high affinity degron recognized by FBXW7 at the C-terminus, loss of interaction with FBXW7, reduced ubiquitination and degradation, and increased NOTCH2 levels. Bone marrow cells derived from HJCYS patients have an enhanced capacity of osteoclastogenesis due to sustained NOTCH2 activity (PubMed:29149593). {ECO:0000269|PubMed:21378989, ECO:0000269|PubMed:29149593}.; ","FUNCTION: Functions as a receptor for membrane-bound ligands Jagged-1 (JAG1), Jagged-2 (JAG2) and Delta-1 (DLL1) to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus (PubMed:21378985, PubMed:21378989). Affects the implementation of differentiation, proliferation and apoptotic programs (By similarity). Involved in bone remodeling and homeostasis. In collaboration with RELA/p65 enhances NFATc1 promoter activity and positively regulates RANKL- induced osteoclast differentiation (PubMed:29149593). Positively regulates self-renewal of liver cancer cells (PubMed:25985737). {ECO:0000250|UniProtKB:O35516, ECO:0000269|PubMed:21378985, ECO:0000269|PubMed:21378989, ECO:0000269|PubMed:25985737, ECO:0000269|PubMed:29149593}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Leu1552Phe","c.4656G>T","MODERATE","1552/2471",26,{"$nulls":5},"5","694","515","559","394","618","467","0","0","0","0.2869",{"$nulls":20},"2.019913","-2.27","2.78","0.999997","-2.71","1.0","0.012","0.575",{"$nulls":3},"Unknown",-1,"AD","Alagille syndrome 2","Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal","COSMIC,kNOTCH",null,null,"C1857761| C0917715","0/0","686,0","0","686","0/1","367,145","0.2832","512",null,"chr1:119923840:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2893"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","NOTCH2","chr1:119923840","NOTCH2(L1552F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Alagille syndrome 2 (ALGS2) [MIM:610205]: A form of Alagille syndrome, an autosomal dominant multisystem disorder. It is clinically defined by hepatic bile duct paucity and cholestasis in association with cardiac, skeletal, and ophthalmologic manifestations. There are characteristic facial features and less frequent clinical involvement of the renal and vascular systems. {ECO:0000269|PubMed:16773578}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hajdu-Cheney syndrome (HJCYS) [MIM:102500]: A rare, autosomal dominant skeletal disorder characterized by the association of facial anomalies, acro-osteolysis, general osteoporosis, insufficient ossification of the skull, and periodontal disease (premature loss of permanent teeth). Other features include cleft palate, congenital heart defects, polycystic kidneys, orthopedic problems and anomalies of the genitalia, intestines and eyes. {ECO:0000269|PubMed:21378985, ECO:0000269|PubMed:21378989, ECO:0000269|PubMed:21681853, ECO:0000269|PubMed:21712856, ECO:0000269|PubMed:21793104, ECO:0000269|PubMed:23389697, ECO:0000269|PubMed:29149593}. Note=The disease is caused by mutations affecting the gene represented in this entry. NOTCH2 nonsense and frameshift mutations associated with Hajdu-Cheney syndrome cluster to the last coding exon of the gene. Mutant mRNA products escape nonsense-mediated decay and the resulting truncated NOTCH2 proteins act in a gain-of-function manner (PubMed:21378989). The pathological mechanism at cellular level involves disruption of a high affinity degron recognized by FBXW7 at the C-terminus, loss of interaction with FBXW7, reduced ubiquitination and degradation, and increased NOTCH2 levels. Bone marrow cells derived from HJCYS patients have an enhanced capacity of osteoclastogenesis due to sustained NOTCH2 activity (PubMed:29149593). {ECO:0000269|PubMed:21378989, ECO:0000269|PubMed:29149593}.; ","FUNCTION: Functions as a receptor for membrane-bound ligands Jagged-1 (JAG1), Jagged-2 (JAG2) and Delta-1 (DLL1) to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus (PubMed:21378985, PubMed:21378989). Affects the implementation of differentiation, proliferation and apoptotic programs (By similarity). Involved in bone remodeling and homeostasis. In collaboration with RELA/p65 enhances NFATc1 promoter activity and positively regulates RANKL- induced osteoclast differentiation (PubMed:29149593). Positively regulates self-renewal of liver cancer cells (PubMed:25985737). {ECO:0000250|UniProtKB:O35516, ECO:0000269|PubMed:21378985, ECO:0000269|PubMed:21378989, ECO:0000269|PubMed:25985737, ECO:0000269|PubMed:29149593}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Leu1552Phe","c.4656G>T","MODERATE","1552/2471",26,{"$nulls":5},"5","694","744","559","568","618","667","0","0","0","0.5067",{"$nulls":20},"2.019913","-2.27","2.78","0.999997","-2.71","1.0","0.012","0.575",{"$nulls":3},"Unknown",-1,"AD","Alagille syndrome 2","Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal","COSMIC,kNOTCH",null,null,"C1857761| C0917715","0/0","686,0","0","686","0/1","363,364","0.5007","727",null,"chr1:119923840:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4982"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","NXN","chr17:822359","NXN(D237E)",null,null,"domain (Thioredoxin ), sequence variant (In RRS2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a redox-dependent negative regulator of the Wnt signaling pathway, possibly by preventing ubiquitination of DVL3 by the BCR(KLHL12) complex. May also function as a transcriptional regulator act as a regulator of protein phosphatase 2A (PP2A) (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp237Glu","c.711C>G","MODERATE","237/435",4,{"$nulls":5},"5","805","611","632","464","632","474","0","0","0","0.1224",{"$nulls":20},"4.51866","-2.07",".;2.185","1",".;-3.85",".;0.997",".;0.0","0.939;0.936",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193143","0/0","790,0","0","790","0/1","533,69","0.1146","602",null,"chr17:822359:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1207"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","NXN","chr17:822359","NXN(D237E)",null,null,"domain (Thioredoxin ), sequence variant (In RRS2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a redox-dependent negative regulator of the Wnt signaling pathway, possibly by preventing ubiquitination of DVL3 by the BCR(KLHL12) complex. May also function as a transcriptional regulator act as a regulator of protein phosphatase 2A (PP2A) (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp237Glu","c.711C>G","MODERATE","237/435",4,{"$nulls":5},"4","805","2162","632","1595","634","1756","0","0","0","0.09",{"$nulls":20},"4.51866","-2.07",".;2.185","1",".;-3.85",".;0.997",".;0.0","0.939;0.936",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193143","0/0","778,0","0","778","0/1","1842,163","0.0813","2005",null,"chr17:822359:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.074"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","OR14I1","chr1:248682186","OR14I1(N40I)",null,null,"transmembrane region (Helical; Name=1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn40Ile","c.119A>T","MODERATE","40/311",1,{"$nulls":5},"5","224","269","181","222","210","235","0","0","0","0.1149",{"$nulls":20},"2.370419","-0.96","4.22","0.582452","-8.95","1.0",null,"0.601",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","225,0","0","225","0/1","240,28","0.1045","268",null,"chr1:248682186:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1081"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","OR2D3","chr11:6921257","OR2D3(D86Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asp86Tyr","c.256G>T","MODERATE","86/330",1,{"$nulls":5},"5","906","525","697","401","381","216","0","0","0","0.2361",{"$nulls":20},"3.846142","5.21","4.5","0.999914","-8.21","0.998",null,"0.724",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","916,0","0","916","0/1","461,56","0.1083","517",null,"chr11:6921257:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1147"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","OR2D3","chr11:6921257","OR2D3(D86Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asp86Tyr","c.256G>T","MODERATE","86/330",1,{"$nulls":5},"5","906","512","697","394","381","220","0","0","0","0.6455",{"$nulls":20},"3.846142","5.21","4.5","0.999914","-8.21","0.998",null,"0.724",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","917,0","0","917","0/1","344,166","0.3255","510",null,"chr11:6921257:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3173"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ORC5","chr7:104188276","ORC5(R220Q)",{"$nulls":6},255,"PASS","Missense","rs914482359",-1,null,"FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent. The specific DNA sequences that define origins of replication have not been identified yet. ORC is required to assemble the pre- replication complex necessary to initiate DNA replication.; ",{"$nulls":4},"p.Arg220Gln","c.659G>A","MODERATE","220/435",6,{"$nulls":5},"5","273","155","220","112","144","82","0","0","0","0.1707",{"$nulls":20},"4.030483","1.6;0.01","2.645","1","-3.49;-3.47","0.999;1.0","0.005;0.004","0.88;0.887",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","269,0","0","269","0/1","134,16","0.1067","150",null,"chr7:104188276:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.125"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ORC5","chr7:104188276","ORC5(R220Q)",{"$nulls":6},255,"PASS","Missense","rs914482359",-1,null,"FUNCTION: Component of the origin recognition complex (ORC) that binds origins of replication. DNA-binding is ATP-dependent. The specific DNA sequences that define origins of replication have not been identified yet. ORC is required to assemble the pre- replication complex necessary to initiate DNA replication.; ",{"$nulls":4},"p.Arg220Gln","c.659G>A","MODERATE","220/435",6,{"$nulls":5},"5","273","147","220","119","144","88","0","0","0","0.3068",{"$nulls":20},"4.030483","1.6;0.01","2.645","1","-3.49;-3.47","0.999;1.0","0.005;0.004","0.88;0.887",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","268,0","0","268","0/1","110,36","0.2466","146",null,"chr7:104188276:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2521"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","OVCH2","chr11:7695083","OVCH2(Q463P)",null,null,"domain (CUB 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln463Pro","c.1388A>C","MODERATE","463/565",12,{"$nulls":5},"4","610","362","447","255",null,null,"0","0",{"$nulls":22},"2.888027",null,null,"0.83358",{"$nulls":3},"0.563;0.562",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","602,0","0","602","0/1","315,21","0.0625","336",null,"chr11:7695083:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0549"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PARD3","chr10:34337295","PARD3(S850*)",null,null,"region of interest (Interaction with PRKCI and PRKCZ ), splice variant (In isoform 3, isoform 6, isoform 7, isoform 9 and isoform 10. )","modified-residue:phosphoserine","MODERATE",null,255,"PASS","Loss Of Function",null,-1,"DISEASE: Neural tube defects (NTD) [MIM:182940]: Congenital malformations of the central nervous system and adjacent structures related to defective neural tube closure during the first trimester of pregnancy. Failure of neural tube closure can occur at any level of the embryonic axis. Common NTD forms include anencephaly, myelomeningocele and spina bifida, which result from the failure of fusion in the cranial and spinal region of the neural tube. NTDs have a multifactorial etiology encompassing both genetic and environmental components. {ECO:0000269|PubMed:27925688}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Adapter protein involved in asymmetrical cell division and cell polarization processes (PubMed:27925688, PubMed:10954424). Seems to play a central role in the formation of epithelial tight junctions (PubMed:27925688). Targets the phosphatase PTEN to cell junctions (By similarity). Involved in Schwann cell peripheral myelination (By similarity). Association with PARD6B may prevent the interaction of PARD3 with F11R/JAM1, thereby preventing tight junction assembly (By similarity). The PARD6-PARD3 complex links GTP-bound Rho small GTPases to atypical protein kinase C proteins (PubMed:10934474). Required for establishment of neuronal polarity and normal axon formation in cultured hippocampal neurons (PubMed:19812038, PubMed:27925688). {ECO:0000250|UniProtKB:Q99NH2, ECO:0000250|UniProtKB:Q9Z340, ECO:0000269|PubMed:10934474, ECO:0000269|PubMed:10954424, ECO:0000269|PubMed:19812038, ECO:0000269|PubMed:27925688}.; ",{"$nulls":4},"p.Ser850*","c.2549C>G","HIGH","850/1356",17,1,{"$nulls":4},"5","267","182","201","137","217","127","0","0","0","0.126",{"$nulls":5},"(PARD3|ENSG00000148498|1|1.00)","(PARD3|ENSG00000148498|1|1.00)",{"$nulls":13},"8.178259",null,null,"1",{"$nulls":3},"0.976;0.982;0.979;0.935;0.907;0.934;0.97;0.922",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","265,0","0","265","0/1","156,21","0.1186","177",null,"chr10:34337295:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1095"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PASK","chr2:241135948","PASK(D410G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine-protein kinase involved in energy homeostasis and protein translation. Phosphorylates EEF1A1, GYS1, PDX1 and RPS6. Probably plays a role under changing environmental conditions (oxygen, glucose, nutrition), rather than under standard conditions. Acts as a sensor involved in energy homeostasis: regulates glycogen synthase synthesis by mediating phosphorylation of GYS1, leading to GYS1 inactivation. May be involved in glucose-stimulated insulin production in pancreas and regulation of glucagon secretion by glucose in alpha cells; however such data require additional evidences. May play a role in regulation of protein translation by phosphorylating EEF1A1, leading to increase translation efficiency. May also participate to respiratory regulation. {ECO:0000269|PubMed:16275910, ECO:0000269|PubMed:17052199, ECO:0000269|PubMed:17595531, ECO:0000269|PubMed:20943661, ECO:0000269|PubMed:21181396, ECO:0000269|PubMed:21418524}.; ",{"$nulls":4},"p.Asp410Gly","c.1229A>G","MODERATE","410/1330",8,{"$nulls":5},"5","635","373","480","274","542","323","0","0","0","0.096",{"$nulls":20},"1.039923","-0.56;.;-0.56;-0.51;0.44","2.085","1;1;1;1;0.999999;1","-3.22;.;-3.22;-3.22;-3.29","0.114;0.114;0.114;0.587;.","0.001;.;0.001;0.001;0.001","0.487;0.504;0.444;0.402;0.446",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","625,0","0","625","0/1","311,42","0.119","353",null,"chr2:241135948:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1277"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PCDHA4","chr5:140809117","PCDHA4(R644C)",{"$nulls":6},255,"PASS","Missense","rs142688560",0.001511627906976744,null,"FUNCTION: Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain. {ECO:0000250|UniProtKB:O88689}.; ",{"$nulls":4},"p.Arg644Cys","c.1930C>T","MODERATE","644/947",1,{"$nulls":5},"4","2634","1340","2062","965","2234","1163","0","0","0","0.5417",{"$nulls":20},"3.005803",".;.;0.63;0.63",".;2.335;.;2.335","0.999998;0.999998;0.999998;0.999998;1;1;1",".;.;-6.63;-6.63",".;1.0;0.999;0.999",".;.;0.001;0.001",".;0.275;0.521;0.546",{"$nulls":3},"ESP6500_EA_AF",0.001511627906976744,{"$nulls":7},"0/0","2406,0","0","2406","0/1","557,625","0.5288","1182",null,"chr5:140809117:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5119"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PFN1","chr17:4948540","PFN1(R31K)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Amyotrophic lateral sclerosis 18 (ALS18) [MIM:614808]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5- 10% of the cases. {ECO:0000269|PubMed:22801503}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG. Inhibits androgen receptor (AR) and HTT aggregation and binding of G-actin is essential for its inhibition of AR. {ECO:0000269|PubMed:18573880}.; ",{"$nulls":4},"p.Arg31Lys","c.92G>A","MODERATE","31/164",2,{"$nulls":5},"4","161","87","143","68",null,null,"0","0",{"$nulls":22},"1.497112","-1.39",null,"1",{"$nulls":7},"Unknown",-1,"AD","Amyotrophic lateral sclerosis 18","Neurologic",{"$nulls":3},"C3553719","0/0","157,0","0","157","0/1","73,12","0.1412","85",null,"chr17:4948540:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1471"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PFN1","chr17:4948540","PFN1(R31K)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Amyotrophic lateral sclerosis 18 (ALS18) [MIM:614808]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5- 10% of the cases. {ECO:0000269|PubMed:22801503}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG. Inhibits androgen receptor (AR) and HTT aggregation and binding of G-actin is essential for its inhibition of AR. {ECO:0000269|PubMed:18573880}.; ",{"$nulls":4},"p.Arg31Lys","c.92G>A","MODERATE","31/164",2,{"$nulls":5},"5","161","119","143","101","145","99","0","0","0","0.2727",{"$nulls":20},"1.497112","-1.39",null,"1",{"$nulls":7},"Unknown",-1,"AD","Amyotrophic lateral sclerosis 18","Neurologic",{"$nulls":3},"C3553719","0/0","158,0","0","158","0/1","76,36","0.3214","112",null,"chr17:4948540:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3168"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PLB1","chr2:28630629","PLB1(K1288E)",null,null,"topological domain (Extracellular ), repeat (4 ), region of interest (4 X 308-326 AA approximate repeats ), splice variant (In isoform 4. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Membrane-associated phospholipase. Exhibits a calcium- independent broad substrate specificity including phospholipase A2/lysophospholipase activity. Preferential hydrolysis at the sn-2 position of diacylphospholipids and diacyglycerol, whereas it shows no positional specificity toward triacylglycerol. Exhibits also esterase activity toward p-nitrophenyl. May act on the brush border membrane to facilitate the absorption of digested lipids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Lys1288Glu","c.3862A>G","MODERATE","1288/1458",54,{"$nulls":5},"5","259","147","209","112","217","109","0","0","0","0.1468",{"$nulls":20},"2.30093","2.58","1.24;.","1","-0.73;-0.79","0.709;0.523","0.436;0.385","0.272;0.265",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","257,0","0","257","0/1","119,16","0.1185","135",null,"chr2:28630629:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1071"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PLCE1","chr10:94031280","PLCE1(E78D)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Nephrotic syndrome 3 (NPHS3) [MIM:610725]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. Most patients with NPHS3 show diffuse mesangial sclerosis on renal biopsy, which is a pathologic entity characterized by mesangial matrix expansion with no mesangial hypercellularity, hypertrophy of the podocytes, vacuolized podocytes, thickened basement membranes, and diminished patency of the capillary lumen. {ECO:0000269|PubMed:17086182}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. PLCE1 is a bifunctional enzyme which also regulates small GTPases of the Ras superfamily through its Ras guanine- exchange factor (RasGEF) activity. As an effector of heterotrimeric and small G-protein, it may play a role in cell survival, cell growth, actin organization and T-cell activation. {ECO:0000269|PubMed:11022047, ECO:0000269|PubMed:11395506, ECO:0000269|PubMed:11715024, ECO:0000269|PubMed:11877431, ECO:0000269|PubMed:12721365, ECO:0000269|PubMed:16537651, ECO:0000269|PubMed:17086182}.; ",{"$nulls":4},"p.Glu78Asp","c.234G>T","MODERATE","78/2302",1,{"$nulls":5},"5","421","181","354","145","364","152","0","0","0","0.2171",{"$nulls":20},"1.5267819999999999","-0.58","0.975","0.999989","-0.39","0.034","0.07","0.113",{"$nulls":3},"Unknown",-1,"AR","Nephrotic syndrome, type 3","Renal",{"$nulls":3},"C1853124","0/0","421,0","0","421","0/1","144,36","0.2","180",null,"chr10:94031280:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2138"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PLCE1","chr10:94031280","PLCE1(E78D)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Nephrotic syndrome 3 (NPHS3) [MIM:610725]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. Most patients with NPHS3 show diffuse mesangial sclerosis on renal biopsy, which is a pathologic entity characterized by mesangial matrix expansion with no mesangial hypercellularity, hypertrophy of the podocytes, vacuolized podocytes, thickened basement membranes, and diminished patency of the capillary lumen. {ECO:0000269|PubMed:17086182}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. PLCE1 is a bifunctional enzyme which also regulates small GTPases of the Ras superfamily through its Ras guanine- exchange factor (RasGEF) activity. As an effector of heterotrimeric and small G-protein, it may play a role in cell survival, cell growth, actin organization and T-cell activation. {ECO:0000269|PubMed:11022047, ECO:0000269|PubMed:11395506, ECO:0000269|PubMed:11715024, ECO:0000269|PubMed:11877431, ECO:0000269|PubMed:12721365, ECO:0000269|PubMed:16537651, ECO:0000269|PubMed:17086182}.; ",{"$nulls":4},"p.Glu78Asp","c.234G>T","MODERATE","78/2302",1,{"$nulls":5},"5","421","150","354","120","364","128","0","0","0","0.4766",{"$nulls":20},"1.5267819999999999","-0.58","0.975","0.999989","-0.39","0.034","0.07","0.113",{"$nulls":3},"Unknown",-1,"AR","Nephrotic syndrome, type 3","Renal",{"$nulls":3},"C1853124","0/0","421,0","0","421","0/1","83,69","0.4539","152",null,"chr10:94031280:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4667"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PRG4","chr1:186308637","PRG4(I973T)",{"$nulls":6},255,"PASS","Missense","rs1256124498",-1,"DISEASE: Camptodactyly-arthropathy-coxa vara-pericarditis syndrome (CACP) [MIM:208250]: An autosomal recessive disorder characterized by the association of congenital or early-onset camptodactyly and non-inflammatory arthropathy with synovial hyperplasia. Individuals with CACP have normal appearing joints at birth but with advancing age develop joint failure, non-inflammatory synoviocyte hyperplasia and subintimal fibrosis of the synovial capsule. Some patients also manifest progressive coxa vara deformity and/or non-inflammatory pericardial or pleural effusions. {ECO:0000269|PubMed:10545950}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in boundary lubrication within articulating joints. Prevents protein deposition onto cartilage from synovial fluid by controlling adhesion-dependent synovial growth and inhibiting the adhesion of synovial cells to the cartilage surface.; ",{"$nulls":4},"p.Ile973Thr","c.2918T>C","MODERATE","973/1404",7,{"$nulls":5},"5","251","160","186","125","208","129","0","0","0","0.1473",{"$nulls":20},"-0.920761",".;.;3.79;3.82;3.7",".;.;-0.05;.;.","1","-1.3;.;-0.82;-0.88;-0.83",".;.;0.0;0.0;0.0","0.034;.;0.098;0.025;0.027",".;0.101;0.074;0.073;0.365",{"$nulls":3},"Unknown",-1,"AR","Camptodactyly-arthropathy-coxa vara-pericarditis syndrome","Cardiovascular; Musculoskeletal",{"$nulls":3},"C1859690","0/0","248,0","0","248","0/1","136,22","0.1392","158",null,"chr1:186308637:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.12"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PRPF3","chr1:150332692","PRPF3(Q144H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Retinitis pigmentosa 18 (RP18) [MIM:601414]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:11773002, ECO:0000269|PubMed:12714658, ECO:0000269|PubMed:17932117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). {ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28781166, ECO:0000305|PubMed:20595234}.; ",{"$nulls":4},"p.Gln144His","c.432G>C","MODERATE","144/683",5,{"$nulls":5},"5","383","343","322","294","305","265","0","0","0","0.0755",{"$nulls":20},"2.455863","-1.12","2.3","0.999986;0.999986;0.999999","-1.94","0.979","0.111","0.592",{"$nulls":3},"Unknown",-1,"AD","Retinitis pigmentosa 18","Ophthalmologic",{"$nulls":3},"C1832378","0/0","383,0","0","383","0/1","311,22","0.0661","333",null,"chr1:150332692:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.068"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PSMA6","chr14:35310836","PSMA6(R117I)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the 20S core proteasome complex involved in the proteolytic degradation of most intracellular proteins. This complex plays numerous essential roles within the cell by associating with different regulatory particles. Associated with two 19S regulatory particles, forms the 26S proteasome and thus participates in the ATP-dependent degradation of ubiquitinated proteins. The 26S proteasome plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins that could impair cellular functions, and by removing proteins whose functions are no longer required. Associated with the PA200 or PA28, the 20S proteasome mediates ubiquitin-independent protein degradation. This type of proteolysis is required in several pathways including spermatogenesis (20S-PA200 complex) or generation of a subset of MHC class I-presented antigenic peptides (20S-PA28 complex). {ECO:0000269|PubMed:15244466, ECO:0000269|PubMed:27176742, ECO:0000269|PubMed:8610016}.; ",{"$nulls":4},"p.Arg117Ile","c.350G>T","MODERATE","117/252",4,{"$nulls":5},"4","833","605","644","443","708","356","0","0","0","0.3427",{"$nulls":20},"4.646955","1.89;.;1.89;1.89;1.89;1.89",".;.;3.65;.;.;.","1","-7.71;.;-7.29;-7.29;-7.71;-7.77",".;.;0.918;.;.;.","0.011;.;0.01;0.01;0.019;0.011","0.79;0.801;0.789;0.728;0.801;0.787",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1832662","0/0","825,1","0.0012","826","0/1","397,196","0.3305","593",null,"chr14:35310836:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3318"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PTPN21","chr14:88469930","PTPN21(A998S)",null,null,"domain (Tyrosine-protein phosphatase )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala998Ser","c.2992G>T","MODERATE","998/1174",15,{"$nulls":5},"5","558","347","462","266","489","292","0","0","0","0.1301",{"$nulls":20},"2.739623","2.63","0.015","0.929726","-0.99","0.439","0.22","0.297;0.3",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","561,0","0","561","0/1","300,43","0.1254","343",null,"chr14:88469930:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1353"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PTPN21","chr14:88469930","PTPN21(A998S)",null,null,"domain (Tyrosine-protein phosphatase )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala998Ser","c.2992G>T","MODERATE","998/1174",15,{"$nulls":5},"5","558","247","462","185","489","200","0","0","0","0.49",{"$nulls":20},"2.739623","2.63","0.015","0.929726","-0.99","0.439","0.22","0.297;0.3",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","561,0","0","561","0/1","117,118","0.5021","235",null,"chr14:88469930:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4973"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","PXDNL","chr8:51408791","PXDNL(A945T)",null,null,"disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform PMR1: Endonuclease selectively degrading some target mRNAs while they are engaged by translating ribosomes, among which albumin and beta-globin mRNAs. {ECO:0000269|PubMed:22543864}.; ",{"$nulls":4},"p.Ala945Thr","c.2833G>A","MODERATE","945/1463",17,3,{"$nulls":4},"5","843","623","713","493","689","521","0","0","0","0.1132",{"$nulls":20},"-0.062956","-0.7","-0.625","0.999999","0.12",null,"0.382","0.036",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","834,0","0","834","0/1","522,69","0.1168","591",null,"chr8:51408791:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1197"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PXDNL","chr8:51408791","PXDNL(A945T)",null,null,"disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform PMR1: Endonuclease selectively degrading some target mRNAs while they are engaged by translating ribosomes, among which albumin and beta-globin mRNAs. {ECO:0000269|PubMed:22543864}.; ",{"$nulls":4},"p.Ala945Thr","c.2833G>A","MODERATE","945/1463",17,3,{"$nulls":4},"4","843","908","713","710","690","786","0","0","0","0.2112",{"$nulls":20},"-0.062956","-0.7","-0.625","0.999999","0.12",null,"0.382","0.036",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","834,0","0","834","0/1","698,178","0.2032","876",null,"chr8:51408791:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2127"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PXDNL","chr8:51339734","PXDNL(V1346M)",null,null,"splice variant (In isoform PMR1. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform PMR1: Endonuclease selectively degrading some target mRNAs while they are engaged by translating ribosomes, among which albumin and beta-globin mRNAs. {ECO:0000269|PubMed:22543864}.; ",{"$nulls":4},"p.Val1346Met","c.4036G>A","MODERATE","1346/1463",21,{"$nulls":5},"4","451","384","316","253","401","346","0","0","0","0.2081",{"$nulls":20},"0.453665","-0.12","0.41","1","-0.15","0.006","0.236","0.149",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","448,0","0","448","0/1","287,90","0.2387","377",null,"chr8:51339734:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2134"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","PYHIN1","chr1:158937124","PYHIN1(I72L)",null,null,"domain (Pyrin )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Major mediator of the tumor suppressor activity of IFN in breast cancer cells. Promotes ubiquitination and subsequent degradation of MDM2, which leads to p53/TP53 stabilization. Promotes ubiquitination and subsequent degradation of HDAC1, which in turn enhances maspin expression, and impairs invasive activity of cancer cells. {ECO:0000269|PubMed:16479015, ECO:0000269|PubMed:18247378}.; ",{"$nulls":4},"p.Ile72Leu","c.214A>C","MODERATE","72/492",2,{"$nulls":5},"5","300","245","215","165","286","236","0","0","0","0.2627",{"$nulls":20},"1.171403","0.48",".;1.995;1.995;1.995;1.995;1.995","1","-1.23;-0.97;-0.97;-0.93;-0.93;-1.0",".;0.363;0.176;0.082;0.176;0.736","0.137;0.115;0.176;0.072;0.062;0.052",".;0.38;0.378;0.388;0.387;0.421",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","297,0","0","297","0/1","180,62","0.2562","242",null,"chr1:158937124:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2242"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","RBMXL2","chr11:7089583","RBMXL2(R155C)",null,null,"compositionally biased region (Arg/Gly/Pro-rich )",{"$nulls":3},255,"PASS","Missense","rs1263348669",-1,{"$nulls":6},"p.Arg155Cys","c.463C>T","MODERATE","155/392",1,{"$nulls":5},"5","289","167","224","129","240","140","0","0","0","0.15",{"$nulls":20},"3.129981","-1.22","2.28","0.999972","-4.39","0.999",null,"0.376",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","288,0","0","288","0/1","139,25","0.1524","164",null,"chr11:7089583:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1318"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","RBMXL2","chr11:7089583","RBMXL2(R155C)",null,null,"compositionally biased region (Arg/Gly/Pro-rich )",{"$nulls":3},255,"PASS","Missense","rs1263348669",-1,{"$nulls":6},"p.Arg155Cys","c.463C>T","MODERATE","155/392",1,{"$nulls":5},"5","289","202","224","156","241","160","0","0","0","0.3688",{"$nulls":20},"3.129981","-1.22","2.28","0.999972","-4.39","0.999",null,"0.376",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","287,0","0","287","0/1","132,68","0.34","200",null,"chr11:7089583:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3397"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","RCSD1","chr1:167697654","RCSD1(K346fs)",{"$nulls":3},"modified-residue:phosphothreonine","MODERATE",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Stress-induced phosphorylation of CAPZIP may regulate the ability of F-actin-capping protein to remodel actin filament assembly. {ECO:0000269|PubMed:15850461}.; ",{"$nulls":4},"p.Lys346fs","c.1035_1053delGAAGGAGACCCCCCACAGT","HIGH","345/416",6,{"$nulls":5},"5","240","139","218","118","231","121","0","0","0","0.1157",{"$nulls":5},"(RCSD1|ENSG00000198771|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","293,0","0","293","0/1","146,16","0.0988","162",null,"chr1:167697654:GCAGTGAAGGAGACCCCCCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1356"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","RCSD1","chr1:167697654","RCSD1(K346fs)",{"$nulls":3},"modified-residue:phosphothreonine","MODERATE",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Stress-induced phosphorylation of CAPZIP may regulate the ability of F-actin-capping protein to remodel actin filament assembly. {ECO:0000269|PubMed:15850461}.; ",{"$nulls":4},"p.Lys346fs","c.1035_1053delGAAGGAGACCCCCCACAGT","HIGH","345/416",6,{"$nulls":5},"5","240","208","218","182","230","211","0","0","0","0.2322",{"$nulls":5},"(RCSD1|ENSG00000198771|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","293,0","0","293","0/1","189,54","0.2222","243",null,"chr1:167697654:GCAGTGAAGGAGACCCCCCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2912"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","RIBC1","chrX:53428401","RIBC1(K106N)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys106Asn","c.318G>C","MODERATE","106/379",5,{"$nulls":5},"5","641","408","519","312","542","328","0","0","0","0.122",{"$nulls":20},"1.046045","1.87",".;2.3;2.3","1","-1.21;-1.21;-1.24",".;0.936;0.642","0.082;0.056;0.06",".;0.157;0.093",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","632,0","0","632","0/1","352,45","0.1134","397",null,"chrX:53428401:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1218"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","RIBC1","chrX:53428401","RIBC1(K106N)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys106Asn","c.318G>C","MODERATE","106/379",5,{"$nulls":5},"5","641","545","519","416","542","464","0","0","0","0.2371",{"$nulls":20},"1.046045","1.87",".;2.3;2.3","1","-1.21;-1.21;-1.24",".;0.936;0.642","0.082;0.056;0.06",".;0.157;0.093",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","630,0","0","630","0/1","410,120","0.2264","530",null,"chrX:53428401:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2308"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","SENP1","chr12:48074608","SENP1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway (PubMed:10652325, PubMed:15199155, PubMed:16253240, PubMed:16553580, PubMed:21829689, PubMed:21965678, PubMed:23160374, PubMed:24943844, PubMed:25406032, PubMed:29506078). The first is the hydrolysis of an alpha-linked peptide bond at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptides, SUMO1, SUMO2 and SUMO3 leading to the mature form of the proteins. The second is the deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins, by cleaving an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein. Deconjugates SUMO1 from HIPK2 (PubMed:16253240). Deconjugates SUMO1 from HDAC1 and BHLHE40/DEC1, which decreases its transcriptional repression activity (PubMed:21829689). Deconjugates SUMO1 from CLOCK, which decreases its transcriptional activation activity (PubMed:23160374). Deconjugates SUMO2 from MTA1 (PubMed:21965678). Deconjugates SUMO1 from METTL3 (PubMed:29506078). Desumoylates CCAR2 which decreases its interaction with SIRT1 (PubMed:25406032). Deconjugates SUMO1 from GPS2 (PubMed:24943844). {ECO:0000269|PubMed:10652325, ECO:0000269|PubMed:15199155, ECO:0000269|PubMed:16253240, ECO:0000269|PubMed:16553580, ECO:0000269|PubMed:21829689, ECO:0000269|PubMed:21965678, ECO:0000269|PubMed:23160374, ECO:0000269|PubMed:24943844, ECO:0000269|PubMed:25406032, ECO:0000269|PubMed:29506078}.; ",{"$nulls":5},"c.657-1G>C","HIGH",null,7,{"$nulls":5},"5","393","188","347","169","320","169","0","0","0","0.1538",{"$nulls":5},"(SENP1|ENSG00000079387|1|1.00)",{"$nulls":14},"4.802799",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":4},"This gene encodes a cysteine protease that specifically targets members of the small ubiquitin-like modifier (SUMO) protein family. This protease regulates SUMO pathways by deconjugating sumoylated proteins. This protease also functions to process the precursor SUMO proteins into their mature form. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012].",null,null,"0/0","390,0","0","390","0/1","156,27","0.1475","183",null,"chr12:48074608:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1598"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","SENP1","chr12:48074608","SENP1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway (PubMed:10652325, PubMed:15199155, PubMed:16253240, PubMed:16553580, PubMed:21829689, PubMed:21965678, PubMed:23160374, PubMed:24943844, PubMed:25406032, PubMed:29506078). The first is the hydrolysis of an alpha-linked peptide bond at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptides, SUMO1, SUMO2 and SUMO3 leading to the mature form of the proteins. The second is the deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins, by cleaving an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein. Deconjugates SUMO1 from HIPK2 (PubMed:16253240). Deconjugates SUMO1 from HDAC1 and BHLHE40/DEC1, which decreases its transcriptional repression activity (PubMed:21829689). Deconjugates SUMO1 from CLOCK, which decreases its transcriptional activation activity (PubMed:23160374). Deconjugates SUMO2 from MTA1 (PubMed:21965678). Deconjugates SUMO1 from METTL3 (PubMed:29506078). Desumoylates CCAR2 which decreases its interaction with SIRT1 (PubMed:25406032). Deconjugates SUMO1 from GPS2 (PubMed:24943844). {ECO:0000269|PubMed:10652325, ECO:0000269|PubMed:15199155, ECO:0000269|PubMed:16253240, ECO:0000269|PubMed:16553580, ECO:0000269|PubMed:21829689, ECO:0000269|PubMed:21965678, ECO:0000269|PubMed:23160374, ECO:0000269|PubMed:24943844, ECO:0000269|PubMed:25406032, ECO:0000269|PubMed:29506078}.; ",{"$nulls":5},"c.657-1G>C","HIGH",null,7,{"$nulls":5},"5","393","182","347","162","321","154","0","0","0","0.2922",{"$nulls":5},"(SENP1|ENSG00000079387|1|1.00)",{"$nulls":14},"4.802799",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":4},"This gene encodes a cysteine protease that specifically targets members of the small ubiquitin-like modifier (SUMO) protein family. This protease regulates SUMO pathways by deconjugating sumoylated proteins. This protease also functions to process the precursor SUMO proteins into their mature form. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012].",null,null,"0/0","390,0","0","390","0/1","125,54","0.3017","179",null,"chr12:48074608:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3086"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","SERPINI2","chr3:167446444","SERPINI2(S373R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser373Arg","c.1119C>A","MODERATE","373/415",9,{"$nulls":5},"4","742","785","548","560","626","670","0","0","0","0.2015",{"$nulls":20},"0.265847","-1.84;.;-1.84;-1.84;-1.84","-0.425;.;-0.425;-0.425;-0.425","1","-0.19;.;-0.19;-0.19;-0.19","0.001;.;0.001;0.001;0.001","0.412;.;0.412;0.412;0.412","0.178;0.169;0.163;0.163;0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","725,0","0","725","0/1","603,147","0.196","750",null,"chr3:167446444:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1946"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","SHANK1","chr19:50662440","SHANK1(L2012P)",{"$nulls":6},255,"PASS","Missense","rs761920863",4.7260000000000005E-5,null,"FUNCTION: Seems to be an adapter protein in the postsynaptic density (PSD) of excitatory synapses that interconnects receptors of the postsynaptic membrane including NMDA-type and metabotropic glutamate receptors via complexes with GKAP/PSD-95 and Homer, respectively, and the actin-based cytoskeleton. Plays a role in the structural and functional organization of the dendritic spine and synaptic junction.; ",{"$nulls":4},"p.Leu2012Pro","c.6035T>C","MODERATE","2012/2169",25,{"$nulls":5},"5","329","161","274","132","284","139","0","0","0","0.0504",{"$nulls":20},"2.978389","1.56;1.13;1.01;1.11",".;1.245;.;.","0.999996;0.999996;0.999996;0.999996;1","-2.16;-2.21;-2.21;-2.21","0.994;0.92;.;.","0.016;0.078;0.079;0.08","0.392;0.404;0.494;0.433",{"$nulls":3},"ExAC_NFE_AF",4.7260000000000005E-5,{"$nulls":7},"0/0","327,0","0","327","0/1","147,10","0.0637","157",null,"chr19:50662440:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0758"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","SIGLEC1","chr20:3694524","SIGLEC1(R985C)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 10 )",{"$nulls":3},255,"PASS","Missense","rs149531553",2.2758306781975421E-4,null,"FUNCTION: Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells. Preferentially binds to alpha-2,3-linked sialic acid (By similarity). Binds to SPN/CD43 on T-cells (By similarity). May play a role in hemopoiesis. {ECO:0000250}.; ",{"$nulls":4},"p.Arg985Cys","c.2953C>T","MODERATE","985/1709",12,1,{"$nulls":4},"5","685","455","538","341","595","391","0","0","0","0.1381",{"$nulls":20},"3.293252","1.47","2.98","0.994259","-3.22","0.999","0.001","0.434",{"$nulls":3},"ESP6500_AA_AF",2.2758306781975421E-4,{"$nulls":7},"0/0","672,0","0","672","0/1","380,65","0.1461","445",null,"chr20:3694524:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1554"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","SIGLEC1","chr20:3694524","SIGLEC1(R985C)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 10 )",{"$nulls":3},255,"PASS","Missense","rs149531553",2.2758306781975421E-4,null,"FUNCTION: Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells. Preferentially binds to alpha-2,3-linked sialic acid (By similarity). Binds to SPN/CD43 on T-cells (By similarity). May play a role in hemopoiesis. {ECO:0000250}.; ",{"$nulls":4},"p.Arg985Cys","c.2953C>T","MODERATE","985/1709",12,1,{"$nulls":4},"5","685","552","538","389","594","479","0","0","0","0.2965",{"$nulls":20},"3.293252","1.47","2.98","0.994259","-3.22","0.999","0.001","0.434",{"$nulls":3},"ESP6500_AA_AF",2.2758306781975421E-4,{"$nulls":7},"0/0","672,0","0","672","0/1","366,174","0.3222","540",null,"chr20:3694524:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3316"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","SLC6A14","chrX:116446781","SLC6A14(L277H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the uptake of a broad range of neutral and cationic amino acids (with the exception of proline) in a Na(+)/Cl(-)-dependent manner. {ECO:0000269|PubMed:10446133}.; ",{"$nulls":4},"p.Leu277His","c.830T>A","MODERATE","277/642",7,{"$nulls":5},"5","818","806","592","563","711","716","0","0","0","0.2682",{"$nulls":20},"2.817933","-1.09","3.895","0.998312",null,"0.999",null,"0.655",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","789,0","0","789","0/1","566,183","0.2443","749",null,"chrX:116446781:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2487"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","SNX1","chr15:64136358","SNX1(R465K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)) or phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) (PubMed:12198132). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Can sense membrane curvature and has in vitro vesicle- to-membrane remodeling activity (PubMed:19816406, PubMed:23085988). Involved in retrograde endosome-to-TGN transport of lysosomal enzyme receptors (IGF2R, M6PR and SORT1) and Shiginella dysenteria toxin stxB. Plays a role in targeting ligand-activated EGFR to the lysosomes for degradation after endocytosis from the cell surface and release from the Golgi (PubMed:12198132, PubMed:15498486, PubMed:17550970, PubMed:17101778, PubMed:18088323, PubMed:21040701). Involvement in retromer-independent endocytic trafficking of P2RY1 and lysosomal degradation of protease-activated receptor-1/F2R (PubMed:16407403, PubMed:20070609). Promotes KALRN- and RHOG-dependent but retromer- independent membrane remodeling such as lamellipodium formation; the function is dependent on GEF activity of KALRN (PubMed:20604901). Required for endocytosis of DRD5 upon agonist stimulation but not for basal receptor trafficking (PubMed:23152498). {ECO:0000269|PubMed:12198132, ECO:0000269|PubMed:15498486, ECO:0000269|PubMed:16407403, ECO:0000269|PubMed:17101778, ECO:0000269|PubMed:17550970, ECO:0000269|PubMed:18088323, ECO:0000269|PubMed:19816406, ECO:0000269|PubMed:20070609, ECO:0000269|PubMed:20604901, ECO:0000269|PubMed:21040701, ECO:0000269|PubMed:23085988, ECO:0000269|PubMed:23152498, ECO:0000303|PubMed:15498486}.; ",{"$nulls":4},"p.Arg465Lys","c.1394G>A","MODERATE","465/557",13,{"$nulls":5},"5","478","247","372","173","410","206","0","0","0","0.1942",{"$nulls":20},"3.489822","0.99;0.99;0.99;0.99;1.72",".;1.835;1.835;.;.","1","-0.56;-0.4;-0.4;-0.47;-0.72",".;.;0.198;0.675;.","0.568;0.321;0.298;0.34;0.127","0.594;0.576;0.561;0.596;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","466,0","0","466","0/1","189,45","0.1923","234",null,"chr15:64136358:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2023"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","SNX1","chr15:64136358","SNX1(R465K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)) or phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) (PubMed:12198132). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Can sense membrane curvature and has in vitro vesicle- to-membrane remodeling activity (PubMed:19816406, PubMed:23085988). Involved in retrograde endosome-to-TGN transport of lysosomal enzyme receptors (IGF2R, M6PR and SORT1) and Shiginella dysenteria toxin stxB. Plays a role in targeting ligand-activated EGFR to the lysosomes for degradation after endocytosis from the cell surface and release from the Golgi (PubMed:12198132, PubMed:15498486, PubMed:17550970, PubMed:17101778, PubMed:18088323, PubMed:21040701). Involvement in retromer-independent endocytic trafficking of P2RY1 and lysosomal degradation of protease-activated receptor-1/F2R (PubMed:16407403, PubMed:20070609). Promotes KALRN- and RHOG-dependent but retromer- independent membrane remodeling such as lamellipodium formation; the function is dependent on GEF activity of KALRN (PubMed:20604901). Required for endocytosis of DRD5 upon agonist stimulation but not for basal receptor trafficking (PubMed:23152498). {ECO:0000269|PubMed:12198132, ECO:0000269|PubMed:15498486, ECO:0000269|PubMed:16407403, ECO:0000269|PubMed:17101778, ECO:0000269|PubMed:17550970, ECO:0000269|PubMed:18088323, ECO:0000269|PubMed:19816406, ECO:0000269|PubMed:20070609, ECO:0000269|PubMed:20604901, ECO:0000269|PubMed:21040701, ECO:0000269|PubMed:23085988, ECO:0000269|PubMed:23152498, ECO:0000303|PubMed:15498486}.; ",{"$nulls":4},"p.Arg465Lys","c.1394G>A","MODERATE","465/557",13,{"$nulls":5},"5","478","197","372","144","408","172","0","0","0","0.5058",{"$nulls":20},"3.489822","0.99;0.99;0.99;0.99;1.72",".;1.835;1.835;.;.","1","-0.56;-0.4;-0.4;-0.47;-0.72",".;.;0.198;0.675;.","0.568;0.321;0.298;0.34;0.127","0.594;0.576;0.561;0.596;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","470,0","0","470","0/1","97,97","0.5","194",null,"chr15:64136358:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5208"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","SNX6","chr14:34597598","SNX6(F200del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes phosphatidylinositol 3,4-bisphosphate and/or phosphatidylinositol 4,5-bisphosphate (Probable). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex (PubMed:19935774). The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Does not have in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Involved in retrograde endosome-to-TGN transport of lysosomal enzyme receptor IGF2R (PubMed:17148574). May function as link between transport vesicles and dynactin (Probable). Negatively regulates retrograde transport of BACE1 from the cell surface to the trans-Golgi network (PubMed:20354142). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). In association with GIT1 involved in EGFR degradation. Promotes lysosomal degradation of CDKN1B (By similarity). May contribute to transcription regulation (Probable). {ECO:0000250|UniProtKB:Q6P8X1, ECO:0000269|PubMed:17148574, ECO:0000269|PubMed:19935774, ECO:0000269|PubMed:20354142, ECO:0000269|PubMed:23085988, ECO:0000269|PubMed:24610942, ECO:0000303|PubMed:19935774, ECO:0000303|PubMed:20830743, ECO:0000305}.; ",{"$nulls":4},"p.Phe200del","c.597_599delCTT","MODERATE","199/418",7,{"$nulls":5},"4",null,null,"83","28","99","33",null,null,"0","0.0909",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","122,0","0","122","0/1","33,6","0.1538","39",null,"chr14:34597598:AAAG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1429"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","STXBP5","chr6:147327154","STXBP5(A653G)",null,null,"repeat (WD 10 )",{"$nulls":3},255,"PASS","Missense","rs767372724",1.5000000000000002E-5,null,"FUNCTION: Plays a regulatory role in calcium-dependent exocytosis and neurotransmitter release. Inhibits membrane fusion between transport vesicles and the plasma membrane. May modulate the assembly of trans-SNARE complexes between transport vesicles and the plasma membrane. Inhibits translocation of GLUT4 from intracellular vesicles to the plasma membrane. Competes with STXBP1 for STX1 binding (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala653Gly","c.1958C>G","MODERATE","653/1151",18,{"$nulls":5},"5","735","611","564","446","616","527","0","0","0","0.3055",{"$nulls":20},"3.084708","2.43;2.33;1.57","2.16","1","-3.42;-3.42;-3.39","0.961;0.165;.","0.0","0.7;0.677;0.68",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,{"$nulls":7},"0/0","718,0","0","718","0/1","409,176","0.3009","585",null,"chr6:147327154:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3004"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","SUGP1","chr19:19302281","SUGP1(E291K)",null,null,"repeat (SURP motif 2 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in pre-mRNA splicing.; ",{"$nulls":4},"p.Glu291Lys","c.871G>A","MODERATE","291/645",7,{"$nulls":5},"4","411","260",null,null,"311","202","0","0","0","0.0842",{"$nulls":20},"3.087921","1.12","1.635","0.999998;1","-1.53","0.98","0.015","0.487",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","410,0","0","410","0/1","240,17","0.0661","257",null,"chr19:19302281:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","TAS2R16","chr7:122994846","TAS2R16(A263fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Gustducin-coupled receptor implicated in the perception of bitter compounds in the oral cavity and the gastrointestinal tract. Signals through PLCB2 and the calcium-regulated cation channel TRPM5. {ECO:0000269|PubMed:12379855, ECO:0000269|PubMed:15759003}.; ",{"$nulls":4},"p.Ala263fs","c.788delC","HIGH","263/291",1,{"$nulls":5},"5","306","177","256","139","269","155","0","0","0","0.2903",{"$nulls":5},"(TAS2R16|ENSG00000128519|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":6},"C4693750","0/0","301,0","0","301","0/1","119,53","0.3081","172",null,"chr7:122994846:AG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3094"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","THBS1","chr15:39589958","THBS1(D694H)",null,null,"repeat (TSP type-3 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Binds heparin. May play a role in dentinogenesis and/or maintenance of dentin and dental pulp (By similarity). Ligand for CD36 mediating antiangiogenic properties. Plays a role in ER stress response, via its interaction with the activating transcription factor 6 alpha (ATF6) which produces adaptive ER stress response factors (By similarity). {ECO:0000250, ECO:0000269|PubMed:11134179, ECO:0000269|PubMed:15014436}.; ","gedi|level2",{"$nulls":3},"p.Asp694His","c.2080G>C","MODERATE","694/1170",13,{"$nulls":5},"5","761","322","535","225","701","299","0","0","0","0.1538",{"$nulls":20},"4.495057","-5.66","4.025","1","-6.24","1.0","0.009","0.947",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kP53,kTGF_BETA",{"$nulls":3},"0/0","752,0","0","752","0/1","267,48","0.1524","315",null,"chr15:39589958:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1467"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","THBS1","chr15:39589958","THBS1(D694H)",null,null,"repeat (TSP type-3 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Binds heparin. May play a role in dentinogenesis and/or maintenance of dentin and dental pulp (By similarity). Ligand for CD36 mediating antiangiogenic properties. Plays a role in ER stress response, via its interaction with the activating transcription factor 6 alpha (ATF6) which produces adaptive ER stress response factors (By similarity). {ECO:0000250, ECO:0000269|PubMed:11134179, ECO:0000269|PubMed:15014436}.; ","gedi|level2",{"$nulls":3},"p.Asp694His","c.2080G>C","MODERATE","694/1170",13,{"$nulls":5},"5","761","322","535","217","698","299","0","0","0","0.505",{"$nulls":20},"4.495057","-5.66","4.025","1","-6.24","1.0","0.009","0.947",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kP53,kTGF_BETA",{"$nulls":3},"0/0","754,0","0","754","0/1","153,157","0.5065","310",null,"chr15:39589958:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4977"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","TP53","chr17:7673802","TP53(R234H)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234C)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234D)), sequence variant (In a sporadic cancer; somatic mutation. TP53(Y234F)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234H)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234N)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234Q)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234S)), strand ",{"$nulls":3},255,"PASS","Missense","rs28934576",9.9403578528827028E-4,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg234His","c.701G>A","MODERATE","234/410",8,1016,{"$nulls":4},"5","382","205","288","150","328","187","0","0","0","0.1925",{"$nulls":20},"3.526684","-7.32;.;.;.;.;.;.;.;-7.32;.;.;-7.32;-7.32;.;.;-7.32;.;.;-7.32",".;.;.;.;.;.;.;.;2.08;.;2.08;2.08;2.08;.;.;2.08;.;.;.","1","-4.61;.;.;.;.;.;.;.;-4.78;.;.;-4.61;-4.61;.;.;-4.78;.;.;-4.31",".;.;.;.;.;.;.;.;0.831;.;0.631;1.0;0.631;.;.;0.831;.;.;.","0.007;.;.;.;.;.;.;.;0.007;.;.;0.008;0.007;.;.;0.007;.;.;0.011","0.954;0.911;0.928;0.934;0.881;0.936;0.919;0.956;0.963;0.956;0.949;0.955;0.949;0.943;0.876;0.965;0.956;0.94;.",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","379,0","0","379","0/1","163,36","0.1809","199",null,"chr17:7673802:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1933"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","TP53","chr17:7673802","TP53(R234H)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234C)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234D)), sequence variant (In a sporadic cancer; somatic mutation. TP53(Y234F)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234H)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234N)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234Q)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234S)), strand ",{"$nulls":3},255,"PASS","Missense","rs28934576",9.9403578528827028E-4,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg234His","c.701G>A","MODERATE","234/410",8,1016,{"$nulls":4},"5","382","232","288","173","329","209","0","0","0","0.6746",{"$nulls":20},"3.526684","-7.32;.;.;.;.;.;.;.;-7.32;.;.;-7.32;-7.32;.;.;-7.32;.;.;-7.32",".;.;.;.;.;.;.;.;2.08;.;2.08;2.08;2.08;.;.;2.08;.;.;.","1","-4.61;.;.;.;.;.;.;.;-4.78;.;.;-4.61;-4.61;.;.;-4.78;.;.;-4.31",".;.;.;.;.;.;.;.;0.831;.;0.631;1.0;0.631;.;.;0.831;.;.;.","0.007;.;.;.;.;.;.;.;0.007;.;.;0.008;0.007;.;.;0.007;.;.;0.011","0.954;0.911;0.928;0.934;0.881;0.936;0.919;0.956;0.963;0.956;0.949;0.955;0.949;0.943;0.876;0.965;0.956;0.94;.",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","379,0","0","379","0/1","71,155","0.6858","226",null,"chr17:7673802:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6879"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","TPBG","chr6:82365094","TPBG(P46fs)",null,null,"topological domain (Extracellular ), compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May function as an inhibitor of Wnt/beta-catenin signaling by indirectly interacting with LRP6 and blocking Wnt3a- dependent LRP6 internalization. {ECO:0000269|PubMed:22100263}.; ",{"$nulls":4},"p.Pro46fs","c.134dupC","HIGH","45/420",2,{"$nulls":5},"4","359","226",null,null,"298","196","0","0","0","0.1378",{"$nulls":5},"(TPBG|ENSG00000146242|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"This gene encodes a leucine-rich transmembrane glycoprotein that may be involved in cell adhesion. The encoded protein is an oncofetal antigen that is specific to trophoblast cells. In adults this protein is highly expressed in many tumor cells and is associated with poor clinical outcome in numerous cancers. Alternate splicing in the 5' UTR results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2009].",null,null,"0|0","368,0","0","368","0|1","201,29","0.1261","230",null,"chr6:82365094:G:GC",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","TPBG","chr6:82365094","TPBG(P46fs)",null,null,"topological domain (Extracellular ), compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May function as an inhibitor of Wnt/beta-catenin signaling by indirectly interacting with LRP6 and blocking Wnt3a- dependent LRP6 internalization. {ECO:0000269|PubMed:22100263}.; ",{"$nulls":4},"p.Pro46fs","c.134dupC","HIGH","45/420",2,{"$nulls":5},"4","359","297",null,null,"298","255","0","0","0","0.298",{"$nulls":5},"(TPBG|ENSG00000146242|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"This gene encodes a leucine-rich transmembrane glycoprotein that may be involved in cell adhesion. The encoded protein is an oncofetal antigen that is specific to trophoblast cells. In adults this protein is highly expressed in many tumor cells and is associated with poor clinical outcome in numerous cancers. Alternate splicing in the 5' UTR results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2009].",null,null,"0|0","368,0","0","368","0|1","201,82","0.2898","283",null,"chr6:82365094:G:GC",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","TUBB2B","chr6:3225187","TUBB2B(A301V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Cortical dysplasia, complex, with other brain malformations 7 (CDCBM7) [MIM:610031]: A malformation of the cortex in which the brain surface is irregular and characterized by an excessive number of small gyri with abnormal lamination. Polymicrogyria is a heterogeneous disorder, considered to be the result of postmigratory abnormal cortical organization. {ECO:0000269|PubMed:19465910, ECO:0000269|PubMed:22333901, ECO:0000269|PubMed:23001566}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Fetal akinesia deformation sequence (FADS) [MIM:208150]: A clinically and genetically heterogeneous group of disorders with congenital malformations related to impaired fetal movement. Clinical features include fetal akinesia, intrauterine growth retardation, polyhydramnios, arthrogryposis, pulmonary hypoplasia, craniofacial abnormalities, and cryptorchidism. {ECO:0000269|PubMed:26732629}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in TUBB2B may be involved in cerebellar ataxia, mental retardation, and dysequilibrium syndrome (CAMRQ). {ECO:0000269|PubMed:28013290}.; ","FUNCTION: Tubulin is the major constituent of microtubules (PubMed:23001566, PubMed:28013290, PubMed:26732629). It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain (By similarity). Plays a critical role in proper axon guidance in both central and peripheral axon tracts (PubMed:23001566). Implicated in neuronal migration (PubMed:19465910). {ECO:0000250, ECO:0000269|PubMed:19465910, ECO:0000269|PubMed:23001566, ECO:0000269|PubMed:26732629, ECO:0000269|PubMed:28013290}.; ",{"$nulls":4},"p.Ala301Val","c.902C>T","MODERATE","301/445",4,{"$nulls":5},"3","24","18","25","20",null,null,"0","0",{"$nulls":22},"3.096293","-1.07","1.31","1","-2.33","0.087",null,"0.702",{"$nulls":3},"Unknown",-1,"AD","Polymicrogyria, asymmetric","Neurologic",null,"The protein encoded by this gene is a beta isoform of tubulin, which binds GTP and is a major component of microtubules. This gene is highly similar to TUBB2A and TUBB2C. Defects in this gene are a cause of asymmetric polymicrogyria. [provided by RefSeq, Mar 2010].  ",null,"C3552236","0/0","24,0","0","24","0/1","7,10","0.5882","17",null,"chr6:3225187:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.5"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","UTP20","chr12:101344724","UTP20(R1527G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in 18S pre-rRNA processing. Associates with U3 snoRNA. {ECO:0000269|PubMed:17498821}.; ",{"$nulls":4},"p.Arg1527Gly","c.4579A>G","MODERATE","1527/2785",36,{"$nulls":5},"5","182","118","126","76","167","107","0","0","0","0.3832",{"$nulls":20},"3.186759","-0.17","2.395","0.999284","-5.07","0.868","0.005","0.714",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","180,0","0","180","0/1","74,43","0.3675","117",null,"chr12:101344724:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3816"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ZAN","chr7:100789314","ZAN(L2442M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds in a species-specific manner to the zona pellucida of the egg. May be involved in gamete recognition and/or signaling.; ",{"$nulls":4},"p.Leu2442Met","c.7324C>A","MODERATE","2442/2812",39,{"$nulls":5},"5","711","428","513","293","634","372","0","0","0","0.1317",{"$nulls":20},"0.503651",null,null,"1",null,"0.606;.;0.606;.",null,"0.165;0.145;0.155;0.164",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","697,0","0","697","0/1","356,51","0.1253","407",null,"chr7:100789314:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.116"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ZAN","chr7:100789314","ZAN(L2442M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds in a species-specific manner to the zona pellucida of the egg. May be involved in gamete recognition and/or signaling.; ",{"$nulls":4},"p.Leu2442Met","c.7324C>A","MODERATE","2442/2812",39,{"$nulls":5},"5","711","479","513","321","633","411","0","0","0","0.292",{"$nulls":20},"0.503651",null,null,"1",null,"0.606;.;0.606;.",null,"0.165;0.145;0.155;0.164",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","698,0","0","698","0/1","309,146","0.3209","455",null,"chr7:100789314:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.324"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ZIC1","chr3:147410420","ZIC1(R103H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Craniosynostosis 6 (CRS6) [MIM:616602]: A form of craniosynostosis, a primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. {ECO:0000269|PubMed:26340333}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a transcriptional activator. Involved in neurogenesis. Plays important roles in the early stage of organogenesis of the CNS, as well as during dorsal spinal cord development and maturation of the cerebellum. Involved in the spatial distribution of mossy fiber (MF) neurons within the pontine gray nucleus (PGN). Plays a role in the regulation of MF axon pathway choice. Promotes MF migration towards ipsilaterally- located cerebellar territories. May have a role in shear flow mechanotransduction in osteocytes. Retains nuclear GLI1 and GLI3 in the cytoplasm. Binds to the minimal GLI-consensus sequence 5'- TGGGTGGTC-3' (By similarity). {ECO:0000250|UniProtKB:P46684}.; ",{"$nulls":4},"p.Arg103His","c.308G>A","MODERATE","103/447",1,2,{"$nulls":4},"4","919","859","737","615","807","769","0.0011","0.0011","0","0.3576",{"$nulls":20},"4.525958","-2.4","2.765","0.999999","-3.01","0.999",null,"0.241",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5231485| C4225269","0/0","903,1","0.0011","904","0/1","520,299","0.3651","819",null,"chr3:147410420:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.348"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ZNF239","chr10:43557782","ZNF239(E100K)",{"$nulls":6},255,"PASS","Missense","rs554146935",-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu100Lys","c.298G>A","MODERATE","100/458",2,{"$nulls":5},"5","776","503","608","391","666","430","0","0","0","0.0581",{"$nulls":20},"2.133125","3.13","0.75","0.986936","0.56","0.982","0.026","0.233;0.152;0.158;0.157",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","766,0","0","766","0/1","468,29","0.0584","497",null,"chr10:43557782:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0563"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ZNF429","chr19:21537804","ZNF429(K584T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys584Thr","c.1751A>C","MODERATE","584/674",4,{"$nulls":5},"5","395","227","302","179","172","107","0","0","0","0.3364",{"$nulls":20},"1.638448","2.25;.","0.69;.","0.999838","-4.49;.","0.011;.","0.002;.","0.173;0.205",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","389,0","0","389","0/1","153,69","0.3108","222",null,"chr19:21537804:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3017"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ZNF507","chr19:32353812","ZNF507(S328G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ser328Gly","c.982A>G","MODERATE","328/957",3,{"$nulls":5},"5","537","358","467","306","458","292","0","0","0","0.1644",{"$nulls":20},"1.985044","3.6;3.28;3.6","2.34;.;2.34","0.588046","-0.99;-0.91;-0.99","0.002;.;0.002","0.163;0.145;0.163","0.234;0.292;0.285",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","535,0","0","535","0/1","297,58","0.1634","355",null,"chr19:32353812:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ZNF507","chr19:32353812","ZNF507(S328G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ser328Gly","c.982A>G","MODERATE","328/957",3,{"$nulls":5},"5","537","306","467","267","458","271","0","0","0","0.3173",{"$nulls":20},"1.985044","3.6;3.28;3.6","2.34;.;2.34","0.588046","-0.99;-0.91;-0.99","0.002;.;0.002","0.163;0.145;0.163","0.234;0.292;0.285",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","536,0","0","536","0/1","213,99","0.3173","312",null,"chr19:32353812:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3109"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ZNF581","chr19:55644825","ZNF581(K85T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys85Thr","c.254A>C","MODERATE","85/197",2,{"$nulls":5},"4","1067","483","896","400","849","414","0","0","0","0.5821",{"$nulls":20},"2.441918","3.2","0.895;.;0.895;0.895","0.984428",".;.;-2.47;.","0.984;.;0.984;0.984",".;.;0.13;.","0.415;.;0.416;0.415",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1059,0","0","1059","0/1","216,262","0.5481","478",null,"chr19:55644825:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.54"]
["02DF","T10","JLPIKTOR_JLPIKTOR_17113002DF","ZSCAN23","chr6:28436049","ZSCAN23(C73F)",null,null,"domain (SCAN box )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Cys73Phe","c.218G>T","MODERATE","73/389",2,1,{"$nulls":4},"5","569","366","461","291","469","295","0","0","0","0.0983",{"$nulls":20},"3.571524","3.21","4.365","0.890101","-9.5","0.995",null,"0.796",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","566,0","0","566","0/1","335,31","0.0847","366",null,"chr6:28436049:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0859"]
["02DF","T11","JLPIKTOR_JLPIKTOR_17113002DF","ZSCAN23","chr6:28436049","ZSCAN23(C73F)",null,null,"domain (SCAN box )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Cys73Phe","c.218G>T","MODERATE","73/389",2,1,{"$nulls":4},"5","569","446","461","359","470","373","0","0","0","0.3271",{"$nulls":20},"3.571524","3.21","4.365","0.890101","-9.5","0.995",null,"0.796",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","565,0","0","565","0/1","296,136","0.3148","432",null,"chr6:28436049:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113002DF","somatic","somatic","JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113002DF/somatic/JLPIKTOR_17113002DF_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113002DF_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3259"]

{"sheet":"04HS","index":2,"n_rows":143,"n_cols":107,"rows_kept":143}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ABL1","chr9:130885259","ABL1(S1009L)",null,null,"region of interest (F-actin-binding ), compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense","rs200523450",9.9403578528827028E-4,"DISEASE: Leukemia, chronic myeloid (CML) [MIM:608232]: A clonal myeloproliferative disorder of a pluripotent stem cell with a specific cytogenetic abnormality, the Philadelphia chromosome (Ph), involving myeloid, erythroid, megakaryocytic, B-lymphoid, and sometimes T-lymphoid cells, but not marrow fibroblasts. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Note=A chromosomal aberration involving ABL1 has been found in patients with chronic myeloid leukemia. Translocation t(9;22)(q34;q11) with BCR. The translocation produces a BCR-ABL found also in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL).; DISEASE: Congenital heart defects and skeletal malformations syndrome (CHDSKM) [MIM:617602]: An autosomal dominant disorder characterized by congenital heart disease with atrial and ventricular septal defects, variable skeletal abnormalities, and failure to thrive. Skeletal defects include pectus excavatum, scoliosis, and finger contractures. Some patient exhibit joint laxity. {ECO:0000269|PubMed:28288113}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Non-receptor tyrosine-protein kinase that plays a role in many key processes linked to cell growth and survival such as cytoskeleton remodeling in response to extracellular stimuli, cell motility and adhesion, receptor endocytosis, autophagy, DNA damage response and apoptosis. Coordinates actin remodeling through tyrosine phosphorylation of proteins controlling cytoskeleton dynamics like WASF3 (involved in branch formation); ANXA1 (involved in membrane anchoring); DBN1, DBNL, CTTN, RAPH1 and ENAH (involved in signaling); or MAPT and PXN (microtubule-binding proteins). Phosphorylation of WASF3 is critical for the stimulation of lamellipodia formation and cell migration. Involved in the regulation of cell adhesion and motility through phosphorylation of key regulators of these processes such as BCAR1, CRK, CRKL, DOK1, EFS or NEDD9. Phosphorylates multiple receptor tyrosine kinases and more particularly promotes endocytosis of EGFR, facilitates the formation of neuromuscular synapses through MUSK, inhibits PDGFRB-mediated chemotaxis and modulates the endocytosis of activated B-cell receptor complexes. Other substrates which are involved in endocytosis regulation are the caveolin (CAV1) and RIN1. Moreover, ABL1 regulates the CBL family of ubiquitin ligases that drive receptor down-regulation and actin remodeling. Phosphorylation of CBL leads to increased EGFR stability. Involved in late-stage autophagy by regulating positively the trafficking and function of lysosomal components. ABL1 targets to mitochondria in response to oxidative stress and thereby mediates mitochondrial dysfunction and cell death. In response to oxidative stress, phosphorylates serine/threonine kinase PRKD2 at 'Tyr-717' (PubMed:28428613). ABL1 is also translocated in the nucleus where it has DNA-binding activity and is involved in DNA-damage response and apoptosis. Many substrates are known mediators of DNA repair: DDB1, DDB2, ERCC3, ERCC6, RAD9A, RAD51, RAD52 or WRN. Activates the proapoptotic pathway when the DNA damage is too severe to be repaired. Phosphorylates TP73, a primary regulator for this type of damage-induced apoptosis. Phosphorylates the caspase CASP9 on 'Tyr-153' and regulates its processing in the apoptotic response to DNA damage. Phosphorylates PSMA7 that leads to an inhibition of proteasomal activity and cell cycle transition blocks. ABL1 acts also as a regulator of multiple pathological signaling cascades during infection. Several known tyrosine-phosphorylated microbial proteins have been identified as ABL1 substrates. This is the case of A36R of Vaccinia virus, Tir (translocated intimin receptor) of pathogenic E.coli and possibly Citrobacter, CagA (cytotoxin- associated gene A) of H.pylori, or AnkA (ankyrin repeat-containing protein A) of A.phagocytophilum. Pathogens can highjack ABL1 kinase signaling to reorganize the host actin cytoskeleton for multiple purposes, like facilitating intracellular movement and host cell exit. Finally, functions as its own regulator through autocatalytic activity as well as through phosphorylation of its inhibitor, ABI1. Regulates T-cell differentiation in a TBX21- dependent manner. Phosphorylates TBX21 on tyrosine residues leading to an enhancement of its transcriptional activator activity (By similarity). {ECO:0000250|UniProtKB:P00520, ECO:0000269|PubMed:10391250, ECO:0000269|PubMed:11971963, ECO:0000269|PubMed:12379650, ECO:0000269|PubMed:12531427, ECO:0000269|PubMed:12672821, ECO:0000269|PubMed:15031292, ECO:0000269|PubMed:15556646, ECO:0000269|PubMed:15657060, ECO:0000269|PubMed:15886098, ECO:0000269|PubMed:16424036, ECO:0000269|PubMed:16678104, ECO:0000269|PubMed:16943190, ECO:0000269|PubMed:17306540, ECO:0000269|PubMed:17623672, ECO:0000269|PubMed:18328268, ECO:0000269|PubMed:18945674, ECO:0000269|PubMed:19891780, ECO:0000269|PubMed:20357770, ECO:0000269|PubMed:20417104, ECO:0000269|PubMed:28428613, ECO:0000269|PubMed:9037071, ECO:0000269|PubMed:9144171, ECO:0000269|PubMed:9461559}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Bosutinib\" , \"Dasatinib\" , \"Imatinib\" , \"Mebendazole\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Imatinib\" , \"Mebendazole\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Imatinib\" , \"Mebendazole\"]","p.Ser1009Leu","c.3026C>T","MODERATE","1009/1149",11,2,{"$nulls":4},"5","381","308","298","258","331","266","0","0","0","0.5827",{"$nulls":20},"2.255336","2.65",".;-0.205","0.995927","-1.39;-1.41",".;0.774","0.221;0.195","0.415;0.34",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,{"$nulls":3},"COSMIC,dcPGX,kCANCER,kCELL_CYCLE,kERBB,vRTK",null,null,"C4539857| C0023473","0/0","364,0","0","364","0/1","129,174","0.5743","303",null,"chr9:130885259:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5775"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ABL1","chr9:130885259","ABL1(S1009L)",null,null,"region of interest (F-actin-binding ), compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense","rs200523450",9.9403578528827028E-4,"DISEASE: Leukemia, chronic myeloid (CML) [MIM:608232]: A clonal myeloproliferative disorder of a pluripotent stem cell with a specific cytogenetic abnormality, the Philadelphia chromosome (Ph), involving myeloid, erythroid, megakaryocytic, B-lymphoid, and sometimes T-lymphoid cells, but not marrow fibroblasts. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Note=A chromosomal aberration involving ABL1 has been found in patients with chronic myeloid leukemia. Translocation t(9;22)(q34;q11) with BCR. The translocation produces a BCR-ABL found also in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL).; DISEASE: Congenital heart defects and skeletal malformations syndrome (CHDSKM) [MIM:617602]: An autosomal dominant disorder characterized by congenital heart disease with atrial and ventricular septal defects, variable skeletal abnormalities, and failure to thrive. Skeletal defects include pectus excavatum, scoliosis, and finger contractures. Some patient exhibit joint laxity. {ECO:0000269|PubMed:28288113}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Non-receptor tyrosine-protein kinase that plays a role in many key processes linked to cell growth and survival such as cytoskeleton remodeling in response to extracellular stimuli, cell motility and adhesion, receptor endocytosis, autophagy, DNA damage response and apoptosis. Coordinates actin remodeling through tyrosine phosphorylation of proteins controlling cytoskeleton dynamics like WASF3 (involved in branch formation); ANXA1 (involved in membrane anchoring); DBN1, DBNL, CTTN, RAPH1 and ENAH (involved in signaling); or MAPT and PXN (microtubule-binding proteins). Phosphorylation of WASF3 is critical for the stimulation of lamellipodia formation and cell migration. Involved in the regulation of cell adhesion and motility through phosphorylation of key regulators of these processes such as BCAR1, CRK, CRKL, DOK1, EFS or NEDD9. Phosphorylates multiple receptor tyrosine kinases and more particularly promotes endocytosis of EGFR, facilitates the formation of neuromuscular synapses through MUSK, inhibits PDGFRB-mediated chemotaxis and modulates the endocytosis of activated B-cell receptor complexes. Other substrates which are involved in endocytosis regulation are the caveolin (CAV1) and RIN1. Moreover, ABL1 regulates the CBL family of ubiquitin ligases that drive receptor down-regulation and actin remodeling. Phosphorylation of CBL leads to increased EGFR stability. Involved in late-stage autophagy by regulating positively the trafficking and function of lysosomal components. ABL1 targets to mitochondria in response to oxidative stress and thereby mediates mitochondrial dysfunction and cell death. In response to oxidative stress, phosphorylates serine/threonine kinase PRKD2 at 'Tyr-717' (PubMed:28428613). ABL1 is also translocated in the nucleus where it has DNA-binding activity and is involved in DNA-damage response and apoptosis. Many substrates are known mediators of DNA repair: DDB1, DDB2, ERCC3, ERCC6, RAD9A, RAD51, RAD52 or WRN. Activates the proapoptotic pathway when the DNA damage is too severe to be repaired. Phosphorylates TP73, a primary regulator for this type of damage-induced apoptosis. Phosphorylates the caspase CASP9 on 'Tyr-153' and regulates its processing in the apoptotic response to DNA damage. Phosphorylates PSMA7 that leads to an inhibition of proteasomal activity and cell cycle transition blocks. ABL1 acts also as a regulator of multiple pathological signaling cascades during infection. Several known tyrosine-phosphorylated microbial proteins have been identified as ABL1 substrates. This is the case of A36R of Vaccinia virus, Tir (translocated intimin receptor) of pathogenic E.coli and possibly Citrobacter, CagA (cytotoxin- associated gene A) of H.pylori, or AnkA (ankyrin repeat-containing protein A) of A.phagocytophilum. Pathogens can highjack ABL1 kinase signaling to reorganize the host actin cytoskeleton for multiple purposes, like facilitating intracellular movement and host cell exit. Finally, functions as its own regulator through autocatalytic activity as well as through phosphorylation of its inhibitor, ABI1. Regulates T-cell differentiation in a TBX21- dependent manner. Phosphorylates TBX21 on tyrosine residues leading to an enhancement of its transcriptional activator activity (By similarity). {ECO:0000250|UniProtKB:P00520, ECO:0000269|PubMed:10391250, ECO:0000269|PubMed:11971963, ECO:0000269|PubMed:12379650, ECO:0000269|PubMed:12531427, ECO:0000269|PubMed:12672821, ECO:0000269|PubMed:15031292, ECO:0000269|PubMed:15556646, ECO:0000269|PubMed:15657060, ECO:0000269|PubMed:15886098, ECO:0000269|PubMed:16424036, ECO:0000269|PubMed:16678104, ECO:0000269|PubMed:16943190, ECO:0000269|PubMed:17306540, ECO:0000269|PubMed:17623672, ECO:0000269|PubMed:18328268, ECO:0000269|PubMed:18945674, ECO:0000269|PubMed:19891780, ECO:0000269|PubMed:20357770, ECO:0000269|PubMed:20417104, ECO:0000269|PubMed:28428613, ECO:0000269|PubMed:9037071, ECO:0000269|PubMed:9144171, ECO:0000269|PubMed:9461559}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Bosutinib\" , \"Dasatinib\" , \"Imatinib\" , \"Mebendazole\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Imatinib\" , \"Mebendazole\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Imatinib\" , \"Mebendazole\"]","p.Ser1009Leu","c.3026C>T","MODERATE","1009/1149",11,2,{"$nulls":4},"5","381","321","298","267","330","287","0","0","0","0.7038",{"$nulls":20},"2.255336","2.65",".;-0.205","0.995927","-1.39;-1.41",".;0.774","0.221;0.195","0.415;0.34",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,{"$nulls":3},"COSMIC,dcPGX,kCANCER,kCELL_CYCLE,kERBB,vRTK",null,null,"C4539857| C0023473","0/0","367,0","0","367","0/1","91,223","0.7102","314",null,"chr9:130885259:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6816"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ADAMTS19","chr5:129679769","ADAMTS19(R832*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Arg832*","c.2494C>T","HIGH","832/1207",17,1,{"$nulls":4},"4","398","213","316","166","158","131","0","0","0","0.5649",{"$nulls":5},"(ADAMTS19|ENSG00000145808|1|1.00)","(ADAMTS19|ENSG00000145808|1|1.00)",{"$nulls":13},"8.382401",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","388,0","0","388","0/1","119,87","0.4223","206",null,"chr5:129679769:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4277"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ADAMTS19","chr5:129679769","ADAMTS19(R832*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Arg832*","c.2494C>T","HIGH","832/1207",17,1,{"$nulls":4},"3","398","247","316","191",null,null,"0","0",{"$nulls":7},"(ADAMTS19|ENSG00000145808|1|1.00)","(ADAMTS19|ENSG00000145808|1|1.00)",{"$nulls":13},"8.382401",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","388,0","0","388","0/1","81,162","0.6667","243",null,"chr5:129679769:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6492"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","AGBL1","chr15:86988034","AGBL1(F1092fs)",null,null,"sequence variant (In FECD8; enriched in the nucleus, decreased TCF4-binding. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes gene-encoded polyglutamates from the carboxy-terminus of target proteins such as MYLK. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5. {ECO:0000250|UniProtKB:Q09M05}.; ",{"$nulls":4},"p.Phe1092fs","c.3270delC","HIGH","1090/1112",24,{"$nulls":5},"4",null,null,"146","119","184","156",null,null,"0","0.0513",{"$nulls":31},"Unknown",-1,"AD","Corneal dystrophy, Fuchs endothelial, 8","Ophthalmologic",null,"Polyglutamylation is a reversible posttranslational modification catalyzed by polyglutamylases that results in the addition of glutamate side chains on the modified protein. This gene encodes a glutamate decarboxylase that catalyzes the deglutamylation of polyglutamylated proteins. Mutations in this gene result in dominant late-onset Fuchs corneal dystrophy. [provided by RefSeq, Nov 2013].  ",null,"C3809798","0/0","209,0","0","209","0/1","165,10","0.0571","175",null,"chr15:86988034:AC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0504"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ALG13","chrX:111684995","ALG13(K92I)",null,null,"region of interest (Glycosyltransferase activity ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Epileptic encephalopathy, early infantile, 36 (EIEE36) [MIM:300884]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. Some EIEE36 patients may present with an abnormal isoelectric focusing of serum transferrin, consistent with a diagnostic classification of congenital disorder of glycosylation type I. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:22492991, ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23934111, ECO:0000269|PubMed:26138355, ECO:0000269|PubMed:27476654}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 1: Possible multifunctional enzyme with both glycosyltransferase and deubiquitinase activities.; ",{"$nulls":4},"p.Lys92Ile","c.275A>T","MODERATE","92/1137",3,{"$nulls":5},"5","199","220","176","192","161","172","0","0","0","0.1279",{"$nulls":20},"3.249706","-1.02;-1.02;.;.;.;.",null,"1;1;0.997089","-2.63;-1.87;.;.;.;.","0.01;0.966;0.925;.;.;.","0.172;0.067;.;.;.;.","0.445;0.371;0.4;0.451;0.355;.",{"$nulls":3},"Unknown",-1,"XL","Congenital disorder of glycosylation, type Is","Allergy/Immunology/Infectious; Biochemical; Hematologic; Neurologic; ",{"$nulls":3},"C0282577| C3550904","0/0","200,0","0","200","0/1","186,28","0.1308","214",null,"chrX:111684995:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1302"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ALG13","chrX:111684995","ALG13(K92I)",null,null,"region of interest (Glycosyltransferase activity ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Epileptic encephalopathy, early infantile, 36 (EIEE36) [MIM:300884]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. Some EIEE36 patients may present with an abnormal isoelectric focusing of serum transferrin, consistent with a diagnostic classification of congenital disorder of glycosylation type I. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:22492991, ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23934111, ECO:0000269|PubMed:26138355, ECO:0000269|PubMed:27476654}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 1: Possible multifunctional enzyme with both glycosyltransferase and deubiquitinase activities.; ",{"$nulls":4},"p.Lys92Ile","c.275A>T","MODERATE","92/1137",3,{"$nulls":5},"4","199","184",null,null,"161","146","0","0","0","0.089",{"$nulls":20},"3.249706","-1.02;-1.02;.;.;.;.",null,"1;1;0.997089","-2.63;-1.87;.;.;.;.","0.01;0.966;0.925;.;.;.","0.172;0.067;.;.;.;.","0.445;0.371;0.4;0.451;0.355;.",{"$nulls":3},"Unknown",-1,"XL","Congenital disorder of glycosylation, type Is","Allergy/Immunology/Infectious; Biochemical; Hematologic; Neurologic; ",{"$nulls":3},"C0282577| C3550904","0/0","200,0","0","200","0/1","164,20","0.1087","184",null,"chrX:111684995:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ANK2","chr4:113240507","ANK2(I239R)",null,null,"repeat (ANK 7 ), splice variant (In isoform 5. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Long QT syndrome 4 (LQT4) [MIM:600919]: A heart disorder characterized by a prolonged QT interval on the ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. Long QT syndrome type 4 shows many atypical features compared to classical long QT syndromes, including pronounced sinus bradycardia, polyphasic T waves and atrial fibrillation. Cardiac repolarization defects may be not as severe as in classical LQT syndromes and prolonged QT interval on EKG is not a consistent feature. {ECO:0000269|PubMed:12571597, ECO:0000269|PubMed:15178757}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: In skeletal muscle, required for proper localization of DMD and DCTN4 and for the formation and/or stability of a special subset of microtubules associated with costameres and neuromuscular junctions. Attaches integral membrane proteins to cytoskeletal elements. Also binds to cytoskeletal proteins. Required for coordinate assembly of Na/Ca exchanger, Na/K ATPase and InsP3 receptor at sarcoplasmic reticulum sites in cardiomyocytes. Required for the coordinated expression of the Na/K ATPase, Na/Ca exchanger and beta-2-spectrin (SPTBN1) in the inner segment of rod photoreceptors (By similarity). Required for expression and targeting of SPTBN1 in neonatal cardiomyocytes and for the regulation of neonatal cardiomyocyte contraction rate (PubMed:12571597). Plays a role in endocytosis and intracellular protein transport. Associates with phosphatidylinositol 3- phosphate (PI3P)-positive organelles and binds dynactin to promote long-range motility of cells. Recruits RABGAP1L to (PI3P)-positive early endosomes, where RABGAP1L inactivates RAB22A, and promotes polarized trafficking to the leading edge of the migrating cells. Part of the ANK2/RABGAP1L complex which is required for the polarized recycling of fibronectin receptor ITGA5 ITGB1 to the plasma membrane that enables continuous directional cell migration (By similarity). {ECO:0000250|UniProtKB:Q8C8R3, ECO:0000269|PubMed:12571597}.; ",{"$nulls":4},"p.Ile239Arg","c.716T>G","MODERATE","239/3957",8,{"$nulls":5},"5","339","303","239","219","259","252","0","0","0","0.4683",{"$nulls":20},"4.427821","-0.16;-0.08;-0.08;-0.08;-0.08;-0.08;-0.08;.",".;.;.;.;0.92;0.92;.;.","1","-6.35;-6.35;-6.35;-6.35;-6.35;-6.76;-6.76;.",".;.;1.0;.;1.0;1.0;.;.","0.0;0.0;0.0;0.0;0.0;0.001;0.001;.",".;.;0.797;.;0.809;0.766;0.787;.",{"$nulls":3},"Unknown",-1,"AD","Long QT syndrome, 4; Cardiac arrhythmia, ankyrin-B-related ","Cardiovascular",null,"This gene encodes a member of the ankyrin family of proteins that link the integral membrane proteins to the underlying spectrin-actin cytoskeleton. Ankyrins play key roles in activities such as cell motility, activation, proliferation, contact and the maintenance of specialized membrane domains. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. The protein encoded by this gene is required for targeting and stability of Na/Ca exchanger 1 in cardiomyocytes. Mutations in this gene cause long QT syndrome 4 and cardiac arrhythmia syndrome. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Dec 2011].",null,"C1970119","0/0","321,0","0","321","0/1","176,125","0.4153","301",null,"chr4:113240507:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4155"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ANK2","chr4:113240507","ANK2(I239R)",null,null,"repeat (ANK 7 ), splice variant (In isoform 5. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Long QT syndrome 4 (LQT4) [MIM:600919]: A heart disorder characterized by a prolonged QT interval on the ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. Long QT syndrome type 4 shows many atypical features compared to classical long QT syndromes, including pronounced sinus bradycardia, polyphasic T waves and atrial fibrillation. Cardiac repolarization defects may be not as severe as in classical LQT syndromes and prolonged QT interval on EKG is not a consistent feature. {ECO:0000269|PubMed:12571597, ECO:0000269|PubMed:15178757}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: In skeletal muscle, required for proper localization of DMD and DCTN4 and for the formation and/or stability of a special subset of microtubules associated with costameres and neuromuscular junctions. Attaches integral membrane proteins to cytoskeletal elements. Also binds to cytoskeletal proteins. Required for coordinate assembly of Na/Ca exchanger, Na/K ATPase and InsP3 receptor at sarcoplasmic reticulum sites in cardiomyocytes. Required for the coordinated expression of the Na/K ATPase, Na/Ca exchanger and beta-2-spectrin (SPTBN1) in the inner segment of rod photoreceptors (By similarity). Required for expression and targeting of SPTBN1 in neonatal cardiomyocytes and for the regulation of neonatal cardiomyocyte contraction rate (PubMed:12571597). Plays a role in endocytosis and intracellular protein transport. Associates with phosphatidylinositol 3- phosphate (PI3P)-positive organelles and binds dynactin to promote long-range motility of cells. Recruits RABGAP1L to (PI3P)-positive early endosomes, where RABGAP1L inactivates RAB22A, and promotes polarized trafficking to the leading edge of the migrating cells. Part of the ANK2/RABGAP1L complex which is required for the polarized recycling of fibronectin receptor ITGA5 ITGB1 to the plasma membrane that enables continuous directional cell migration (By similarity). {ECO:0000250|UniProtKB:Q8C8R3, ECO:0000269|PubMed:12571597}.; ",{"$nulls":4},"p.Ile239Arg","c.716T>G","MODERATE","239/3957",8,{"$nulls":5},"5","339","311","239","217","260","248","0","0","0","0.3911",{"$nulls":20},"4.427821","-0.16;-0.08;-0.08;-0.08;-0.08;-0.08;-0.08;.",".;.;.;.;0.92;0.92;.;.","1","-6.35;-6.35;-6.35;-6.35;-6.35;-6.76;-6.76;.",".;.;1.0;.;1.0;1.0;.;.","0.0;0.0;0.0;0.0;0.0;0.001;0.001;.",".;.;0.797;.;0.809;0.766;0.787;.",{"$nulls":3},"Unknown",-1,"AD","Long QT syndrome, 4; Cardiac arrhythmia, ankyrin-B-related ","Cardiovascular",null,"This gene encodes a member of the ankyrin family of proteins that link the integral membrane proteins to the underlying spectrin-actin cytoskeleton. Ankyrins play key roles in activities such as cell motility, activation, proliferation, contact and the maintenance of specialized membrane domains. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. The protein encoded by this gene is required for targeting and stability of Na/Ca exchanger 1 in cardiomyocytes. Mutations in this gene cause long QT syndrome 4 and cardiac arrhythmia syndrome. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Dec 2011].",null,"C1970119","0/0","322,0","0","322","0/1","197,103","0.3433","300",null,"chr4:113240507:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3502"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","AQP10","chr1:154323283","AQP10(G138A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Water channel required to promote glycerol permeability and water transport across cell membranes. May contribute to water transport in the upper portion of small intestine. Isoform 2 is not permeable to urea and glycerol. {ECO:0000269|PubMed:11573934, ECO:0000269|PubMed:12084581}.; ",{"$nulls":4},"p.Gly138Ala","c.413G>C","MODERATE","138/301",4,{"$nulls":5},"5","601","538","450","441","514","454","0","0","0","0.2004",{"$nulls":20},"4.052002","2.69","2.205","0.990786","-5.78;-5.59","1.0;0.998","0.005;0.001","0.678;0.586",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","593,0","0","593","0/1","419,107","0.2034","526",null,"chr1:154323283:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1882"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","AQP10","chr1:154323283","AQP10(G138A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Water channel required to promote glycerol permeability and water transport across cell membranes. May contribute to water transport in the upper portion of small intestine. Isoform 2 is not permeable to urea and glycerol. {ECO:0000269|PubMed:11573934, ECO:0000269|PubMed:12084581}.; ",{"$nulls":4},"p.Gly138Ala","c.413G>C","MODERATE","138/301",4,{"$nulls":5},"5","601","691","450","560","514","575","0","0","0","0.2696",{"$nulls":20},"4.052002","2.69","2.205","0.990786","-5.78;-5.59","1.0;0.998","0.005;0.001","0.678;0.586",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","593,0","0","593","0/1","500,175","0.2593","675",null,"chr1:154323283:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2429"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","AR","chrX:67721863","AR(S783R)",null,null,"domain (NR LBD ), region of interest (Interaction with LPXN ), region of interest (Interaction with CCAR1 ), region of interest (Interaction with KAT7 ), splice variant (In isoform 3. ), splice variant (In isoform 4. ), sequence variant (In prostate cancer; somatic mutation. AR(S783N)), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Androgen insensitivity syndrome (AIS) [MIM:300068]: An X- linked recessive form of pseudohermaphroditism due end-organ resistance to androgen. Affected males have female external genitalia, female breast development, blind vagina, absent uterus and female adnexa, and abdominal or inguinal testes, despite a normal 46,XY karyotype. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10221770, ECO:0000269|PubMed:10404311, ECO:0000269|PubMed:10458483, ECO:0000269|PubMed:10571951, ECO:0000269|PubMed:10590024, ECO:0000269|PubMed:10690872, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:11744994, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1426313, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:1464650, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:1480178, ECO:0000269|PubMed:1487249, ECO:0000269|PubMed:1569163, ECO:0000269|PubMed:1609793, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:16595706, ECO:0000269|PubMed:1775137, ECO:0000269|PubMed:1999491, ECO:0000269|PubMed:2082179, ECO:0000269|PubMed:2594783, ECO:0000269|PubMed:7537149, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7633398, ECO:0000269|PubMed:7641413, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7962294, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:7981689, ECO:0000269|PubMed:7993455, ECO:0000269|PubMed:8040309, ECO:0000269|PubMed:8096390, ECO:0000269|PubMed:8103398, ECO:0000269|PubMed:8162033, ECO:0000269|PubMed:8224266, ECO:0000269|PubMed:8281140, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8339746, ECO:0000269|PubMed:8413310, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8626869, ECO:0000269|PubMed:8647313, ECO:0000269|PubMed:8683794, ECO:0000269|PubMed:8723113, ECO:0000269|PubMed:8768864, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8830623, ECO:0000269|PubMed:8918984, ECO:0000269|PubMed:8990010, ECO:0000269|PubMed:9001799, ECO:0000269|PubMed:9007482, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9106550, ECO:0000269|PubMed:9160185, ECO:0000269|PubMed:9252933, ECO:0000269|PubMed:9255042, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9328206, ECO:0000269|PubMed:9544375, ECO:0000269|PubMed:9554754, ECO:0000269|PubMed:9610419, ECO:0000269|PubMed:9627582, ECO:0000269|PubMed:9698822, ECO:0000269|PubMed:9851768, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.113, ECO:0000269|Ref.179}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinal and bulbar muscular atrophy X-linked 1 (SMAX1) [MIM:313200]: An X-linked recessive form of spinal muscular atrophy. Spinal muscular atrophy refers to a group of neuromuscular disorders characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMAX1 occurs only in men. Age at onset is usually in the third to fifth decade of life, but earlier involvement has been reported. It is characterized by slowly progressive limb and bulbar muscle weakness with fasciculations, muscle atrophy, and gynecomastia. The disorder is clinically similar to classic forms of autosomal spinal muscular atrophy. {ECO:0000269|PubMed:15851746}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by trinucleotide CAG repeat expansion. In SMAX1 patients the number of Gln ranges from 38 to 62. Longer expansions result in earlier onset and more severe clinical manifestations of the disease.; DISEASE: Note=Defects in AR may play a role in metastatic prostate cancer. The mutated receptor stimulates prostate growth and metastases development despite of androgen ablation. This treatment can reduce primary and metastatic lesions probably by inducing apoptosis of tumor cells when they express the wild-type receptor. {ECO:0000269|PubMed:10363963, ECO:0000269|PubMed:10569618, ECO:0000269|PubMed:1562539, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:17311914, ECO:0000269|PubMed:2260966, ECO:0000269|PubMed:25091737, ECO:0000269|PubMed:8187068, ECO:0000269|PubMed:8274409, ECO:0000269|PubMed:8827083}.; DISEASE: Androgen insensitivity, partial (PAIS) [MIM:312300]: A disorder that is characterized by hypospadias, hypogonadism, gynecomastia, genital ambiguity, normal XY karyotype, and a pedigree pattern consistent with X-linked recessive inheritance. Some patients present azoospermia or severe oligospermia without other clinical manifestations. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10470409, ECO:0000269|PubMed:10502786, ECO:0000269|PubMed:10543676, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:1303262, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1424203, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:2010552, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7649358, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7909256, ECO:0000269|PubMed:7910529, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:8033918, ECO:0000269|PubMed:8097257, ECO:0000269|PubMed:8126121, ECO:0000269|PubMed:8205256, ECO:0000269|PubMed:8281139, ECO:0000269|PubMed:8325932, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8550758, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8823308, ECO:0000269|PubMed:8824883, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9196614, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9329414, ECO:0000269|PubMed:9543136, ECO:0000269|PubMed:9607727, ECO:0000269|PubMed:9768671, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.121}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Steroid hormone receptors are ligand-activated transcription factors that regulate eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Transcription factor activity is modulated by bound coactivator and corepressor proteins like ZBTB7A that recruits NCOR1 and NCOR2 to the androgen response elements/ARE on target genes, negatively regulating androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Transcription activation is also down-regulated by NR0B2. Activated, but not phosphorylated, by HIPK3 and ZIPK/DAPK3. {ECO:0000269|PubMed:14664718, ECO:0000269|PubMed:15563469, ECO:0000269|PubMed:17591767, ECO:0000269|PubMed:17911242, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:19345326, ECO:0000269|PubMed:20812024, ECO:0000269|PubMed:20980437, ECO:0000269|PubMed:25091737}.; ","gedi|foundationOne|level2","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","p.Ser783Arg","c.2349C>A","MODERATE","783/920",6,{"$nulls":5},"4","555","703","405","497","478","593","0","0","0","0.1484",{"$nulls":20},"3.304884",".;-4.06;-4.06",null,"0.992458;0.874819;1",".;-1.53;-2.01",null,".;0.009;0.002","0.665;0.709;0.623",{"$nulls":3},"Unknown",-1,"XL","Androgen insensitivity; Androgen insensitivity, partial","Endocrine; Genitourinary; Neurologic; Oncologic","kCANCER",null,null,"C0039585| C0268301| C2678098| C1839259| C0376358","0/0","528,0","0","528","0/1","577,98","0.1452","675",null,"chrX:67721863:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1549"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","AR","chrX:67721863","AR(S783R)",null,null,"domain (NR LBD ), region of interest (Interaction with LPXN ), region of interest (Interaction with CCAR1 ), region of interest (Interaction with KAT7 ), splice variant (In isoform 3. ), splice variant (In isoform 4. ), sequence variant (In prostate cancer; somatic mutation. AR(S783N)), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Androgen insensitivity syndrome (AIS) [MIM:300068]: An X- linked recessive form of pseudohermaphroditism due end-organ resistance to androgen. Affected males have female external genitalia, female breast development, blind vagina, absent uterus and female adnexa, and abdominal or inguinal testes, despite a normal 46,XY karyotype. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10221770, ECO:0000269|PubMed:10404311, ECO:0000269|PubMed:10458483, ECO:0000269|PubMed:10571951, ECO:0000269|PubMed:10590024, ECO:0000269|PubMed:10690872, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:11744994, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1426313, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:1464650, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:1480178, ECO:0000269|PubMed:1487249, ECO:0000269|PubMed:1569163, ECO:0000269|PubMed:1609793, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:16595706, ECO:0000269|PubMed:1775137, ECO:0000269|PubMed:1999491, ECO:0000269|PubMed:2082179, ECO:0000269|PubMed:2594783, ECO:0000269|PubMed:7537149, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7633398, ECO:0000269|PubMed:7641413, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7962294, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:7981689, ECO:0000269|PubMed:7993455, ECO:0000269|PubMed:8040309, ECO:0000269|PubMed:8096390, ECO:0000269|PubMed:8103398, ECO:0000269|PubMed:8162033, ECO:0000269|PubMed:8224266, ECO:0000269|PubMed:8281140, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8339746, ECO:0000269|PubMed:8413310, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8626869, ECO:0000269|PubMed:8647313, ECO:0000269|PubMed:8683794, ECO:0000269|PubMed:8723113, ECO:0000269|PubMed:8768864, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8830623, ECO:0000269|PubMed:8918984, ECO:0000269|PubMed:8990010, ECO:0000269|PubMed:9001799, ECO:0000269|PubMed:9007482, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9106550, ECO:0000269|PubMed:9160185, ECO:0000269|PubMed:9252933, ECO:0000269|PubMed:9255042, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9328206, ECO:0000269|PubMed:9544375, ECO:0000269|PubMed:9554754, ECO:0000269|PubMed:9610419, ECO:0000269|PubMed:9627582, ECO:0000269|PubMed:9698822, ECO:0000269|PubMed:9851768, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.113, ECO:0000269|Ref.179}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinal and bulbar muscular atrophy X-linked 1 (SMAX1) [MIM:313200]: An X-linked recessive form of spinal muscular atrophy. Spinal muscular atrophy refers to a group of neuromuscular disorders characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMAX1 occurs only in men. Age at onset is usually in the third to fifth decade of life, but earlier involvement has been reported. It is characterized by slowly progressive limb and bulbar muscle weakness with fasciculations, muscle atrophy, and gynecomastia. The disorder is clinically similar to classic forms of autosomal spinal muscular atrophy. {ECO:0000269|PubMed:15851746}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by trinucleotide CAG repeat expansion. In SMAX1 patients the number of Gln ranges from 38 to 62. Longer expansions result in earlier onset and more severe clinical manifestations of the disease.; DISEASE: Note=Defects in AR may play a role in metastatic prostate cancer. The mutated receptor stimulates prostate growth and metastases development despite of androgen ablation. This treatment can reduce primary and metastatic lesions probably by inducing apoptosis of tumor cells when they express the wild-type receptor. {ECO:0000269|PubMed:10363963, ECO:0000269|PubMed:10569618, ECO:0000269|PubMed:1562539, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:17311914, ECO:0000269|PubMed:2260966, ECO:0000269|PubMed:25091737, ECO:0000269|PubMed:8187068, ECO:0000269|PubMed:8274409, ECO:0000269|PubMed:8827083}.; DISEASE: Androgen insensitivity, partial (PAIS) [MIM:312300]: A disorder that is characterized by hypospadias, hypogonadism, gynecomastia, genital ambiguity, normal XY karyotype, and a pedigree pattern consistent with X-linked recessive inheritance. Some patients present azoospermia or severe oligospermia without other clinical manifestations. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10470409, ECO:0000269|PubMed:10502786, ECO:0000269|PubMed:10543676, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:1303262, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1424203, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:2010552, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7649358, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7909256, ECO:0000269|PubMed:7910529, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:8033918, ECO:0000269|PubMed:8097257, ECO:0000269|PubMed:8126121, ECO:0000269|PubMed:8205256, ECO:0000269|PubMed:8281139, ECO:0000269|PubMed:8325932, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8550758, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8823308, ECO:0000269|PubMed:8824883, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9196614, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9329414, ECO:0000269|PubMed:9543136, ECO:0000269|PubMed:9607727, ECO:0000269|PubMed:9768671, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.121}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Steroid hormone receptors are ligand-activated transcription factors that regulate eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Transcription factor activity is modulated by bound coactivator and corepressor proteins like ZBTB7A that recruits NCOR1 and NCOR2 to the androgen response elements/ARE on target genes, negatively regulating androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Transcription activation is also down-regulated by NR0B2. Activated, but not phosphorylated, by HIPK3 and ZIPK/DAPK3. {ECO:0000269|PubMed:14664718, ECO:0000269|PubMed:15563469, ECO:0000269|PubMed:17591767, ECO:0000269|PubMed:17911242, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:19345326, ECO:0000269|PubMed:20812024, ECO:0000269|PubMed:20980437, ECO:0000269|PubMed:25091737}.; ","gedi|foundationOne|level2","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","p.Ser783Arg","c.2349C>A","MODERATE","783/920",6,{"$nulls":5},"4","555","550","405","404","481","472","0","0","0","0.1822",{"$nulls":20},"3.304884",".;-4.06;-4.06",null,"0.992458;0.874819;1",".;-1.53;-2.01",null,".;0.009;0.002","0.665;0.709;0.623",{"$nulls":3},"Unknown",-1,"XL","Androgen insensitivity; Androgen insensitivity, partial","Endocrine; Genitourinary; Neurologic; Oncologic","kCANCER",null,null,"C0039585| C0268301| C2678098| C1839259| C0376358","0/0","527,0","0","527","0/1","428,97","0.1848","525",null,"chrX:67721863:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1757"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ARFGEF2","chr20:49023143","ARFGEF2(S1573C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Periventricular nodular heterotopia 2 (PVNH2) [MIM:608097]: A developmental disorder characterized by the presence of periventricular nodules of cerebral gray matter, resulting from a failure of neurons to migrate normally from the lateral ventricular proliferative zone, where they are formed, to the cerebral cortex. PVNH2 is an autosomal recessive form characterized by microcephaly (small brain), severe developmental delay and recurrent infections. No anomalies extrinsic to the central nervous system, such as dysmorphic features or grossly abnormal endocrine or other conditions, are associated with PVNH2. {ECO:0000269|PubMed:14647276, ECO:0000269|PubMed:23812912, ECO:0000269|PubMed:25160555}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF3 and to a lower extent on ARF5 and ARF6. Promotes the activation of ARF1/ARF5/ARF6 through replacement of GDP with GTP. Involved in the regulation of Golgi vesicular transport. Required for the integrity of the endosomal compartment. Involved in trafficking from the trans-Golgi network (TGN) to endosomes and is required for membrane association of the AP-1 complex and GGA1. Seems to be involved in recycling of the transferrin receptor from recycling endosomes to the plasma membrane. Probably is involved in the exit of GABA(A) receptors from the endoplasmic reticulum. Involved in constitutive release of tumor necrosis factor receptor 1 via exosome-like vesicles; the function seems to involve PKA and specifically PRKAR2B. Proposed to act as A kinase-anchoring protein (AKAP) and may mediate crosstalk between Arf and PKA pathways. {ECO:0000269|PubMed:12051703, ECO:0000269|PubMed:12571360, ECO:0000269|PubMed:15385626, ECO:0000269|PubMed:16477018, ECO:0000269|PubMed:17276987, ECO:0000269|PubMed:18625701, ECO:0000269|PubMed:20360857}.; ",{"$nulls":4},"p.Ser1573Cys","c.4717A>T","MODERATE","1573/1785",35,{"$nulls":5},"4","502","579","343","386","466","513","0","0","0","0.462",{"$nulls":20},"3.9834009999999997","0.47","3.195","1","-4.34","1.0","0.002","0.847",{"$nulls":3},"Unknown",-1,"AR","Heterotopia, periventricular, autosomal recessive","Neurologic",{"$nulls":3},"C1842563","0/0","484,0","0","484","0/1","292,275","0.485","567",null,"chr20:49023143:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4508"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ARFGEF2","chr20:49023143","ARFGEF2(S1573C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Periventricular nodular heterotopia 2 (PVNH2) [MIM:608097]: A developmental disorder characterized by the presence of periventricular nodules of cerebral gray matter, resulting from a failure of neurons to migrate normally from the lateral ventricular proliferative zone, where they are formed, to the cerebral cortex. PVNH2 is an autosomal recessive form characterized by microcephaly (small brain), severe developmental delay and recurrent infections. No anomalies extrinsic to the central nervous system, such as dysmorphic features or grossly abnormal endocrine or other conditions, are associated with PVNH2. {ECO:0000269|PubMed:14647276, ECO:0000269|PubMed:23812912, ECO:0000269|PubMed:25160555}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF3 and to a lower extent on ARF5 and ARF6. Promotes the activation of ARF1/ARF5/ARF6 through replacement of GDP with GTP. Involved in the regulation of Golgi vesicular transport. Required for the integrity of the endosomal compartment. Involved in trafficking from the trans-Golgi network (TGN) to endosomes and is required for membrane association of the AP-1 complex and GGA1. Seems to be involved in recycling of the transferrin receptor from recycling endosomes to the plasma membrane. Probably is involved in the exit of GABA(A) receptors from the endoplasmic reticulum. Involved in constitutive release of tumor necrosis factor receptor 1 via exosome-like vesicles; the function seems to involve PKA and specifically PRKAR2B. Proposed to act as A kinase-anchoring protein (AKAP) and may mediate crosstalk between Arf and PKA pathways. {ECO:0000269|PubMed:12051703, ECO:0000269|PubMed:12571360, ECO:0000269|PubMed:15385626, ECO:0000269|PubMed:16477018, ECO:0000269|PubMed:17276987, ECO:0000269|PubMed:18625701, ECO:0000269|PubMed:20360857}.; ",{"$nulls":4},"p.Ser1573Cys","c.4717A>T","MODERATE","1573/1785",35,{"$nulls":5},"4","502","744","343","485","466","670","0","0","0","0.4299",{"$nulls":20},"3.9834009999999997","0.47","3.195","1","-4.34","1.0","0.002","0.847",{"$nulls":3},"Unknown",-1,"AR","Heterotopia, periventricular, autosomal recessive","Neurologic",{"$nulls":3},"C1842563","0/0","483,0","0","483","0/1","404,326","0.4466","730",null,"chr20:49023143:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4598"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ARID2","chr12:45850302","ARID2(G727R)",null,null,"sequence variant (In CSS6. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Coffin-Siris syndrome 6 (CSS6) [MIM:617808]: A form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported. CSS6 inheritance is autosomal dominant. {ECO:0000269|PubMed:26238514, ECO:0000269|PubMed:28124119, ECO:0000269|PubMed:28884947}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Required for the stability of the SWI/SNF chromatin remodeling complex SWI/SNF-B (PBAF). May be involved in targeting the complex to different genes. May be involved in regulating transcriptional activation of cardiac genes. {ECO:0000269|PubMed:16782067, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.; ","gedi|foundationOne",{"$nulls":3},"p.Gly727Arg","c.2179G>C","MODERATE","727/1835",15,{"$nulls":5},"3","543","749",{"$nulls":4},"0","0",{"$nulls":22},"1.844084","1.51;.;.","0.345;.;.","0.786474;1;0.806847;0.897873","-0.3;-0.56;-0.03","0.026;.;0.039","0.001;0.003;0.003","0.268;0.399;0.283",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4540499","0|0","524,0","0","524","0|1","666,54","0.075","720",null,"chr12:45850302:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ATP11C","chrX:139826816","ATP11C(G15E)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules. Required for B cell differentiation past the pro-B cell stage. Seems to mediate phosphatidylserine (PS) flipping in pro-B cells. May be involved in the transport of cholestatic bile acids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly15Glu","c.44G>A","MODERATE","15/1132",2,{"$nulls":5},"5","215","211","140","136","201","192","0","0","0","0.224",{"$nulls":20},"3.635778","3.33;3.27;3.27",".;2.545;2.545","0.999921","-3.01;-2.97;-2.97",".;0.996;0.999","0.004;0.002;0.002","0.392;0.358;0.36",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4746970","0/0","210,0","0","210","0/1","147,54","0.2687","201",null,"chrX:139826816:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2941"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ATP11C","chrX:139826816","ATP11C(G15E)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules. Required for B cell differentiation past the pro-B cell stage. Seems to mediate phosphatidylserine (PS) flipping in pro-B cells. May be involved in the transport of cholestatic bile acids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly15Glu","c.44G>A","MODERATE","15/1132",2,{"$nulls":5},"5","215","196","140","126","199","189","0","0","0","0.0688",{"$nulls":20},"3.635778","3.33;3.27;3.27",".;2.545;2.545","0.999921","-3.01;-2.97;-2.97",".;0.996;0.999","0.004;0.002;0.002","0.392;0.358;0.36",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4746970","0/0","207,0","0","207","0/1","177,14","0.0733","191",null,"chrX:139826816:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0873"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ATP5I","chr4:674241","ATP5I(P3S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Pro3Ser","c.6_7delGCinsAT","MODERATE","2/69",1,{"$nulls":5},"5","510","245","329","176","445","216","0","0","0","0.4167",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","467,0","0","467","0/1","128,119","0.4818","247",null,"chr4:674241:GC:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4261"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ATP5I","chr4:674241","ATP5I(P3S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Pro3Ser","c.6_7delGCinsAT","MODERATE","2/69",1,{"$nulls":5},"5","510","326","329","243","443","296","0","0","0","0.6014",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","461,0","0","461","0/1","124,205","0.6231","329",null,"chr4:674241:GC:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6091"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","CNTNAP4","chr16:76355375","CNTNAP4(L88P)",null,null,"topological domain (Extracellular ), domain (F5/8 type C ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Presynaptic protein involved in both dopaminergic synaptic transmission and GABAergic system, thereby participating in the structural maturation of inhibitory interneuron synapses. Involved in the dopaminergic synaptic transmission by attenuating dopamine release through a presynaptic mechanism. Also participates in the GABAergic system (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu88Pro","c.263T>C","MODERATE","88/1311",2,{"$nulls":5},"5","121","122","108","100","103","98","0","0","0","0.1224",{"$nulls":20},"4.301073",".;.;.;.;-5.61;-5.61",null,"1",".;.;.;.;-6.29;-6.43","1.0;.;.;.;.;1.0",".;.;.;.;0.0;0.0","0.978;0.914;0.963;0.831;0.963;0.971",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","117,0","0","117","0/1","104,14","0.1186","118",null,"chr16:76355375:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.11"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","COL12A1","chr6:75175299","COL12A1(P817T)",null,null,"domain (Fibronectin type-III 5 ), splice variant (In isoform 2. )","domain:Fibronectin_type-III_5","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Ullrich congenital muscular dystrophy 2 (UCMD2) [MIM:616470]: A form of Ullrich muscular dystrophy, a congenital myopathy characterized by muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course is more severe than in Bethlem myopathy. {ECO:0000269|PubMed:24334604}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bethlem myopathy 2 (BTHLM2) [MIM:616471]: A form of Bethlem myopathy, a benign proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles. BTHLM2 inheritance is autosomal dominant. {ECO:0000269|PubMed:24334604, ECO:0000269|PubMed:24334769}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type XII collagen interacts with type I collagen- containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix. {ECO:0000250}.; ",{"$nulls":4},"p.Pro817Thr","c.2449C>A","MODERATE","817/3063",13,{"$nulls":5},"5","291","192","206","143","278","172","0","0","0","0.2733",{"$nulls":20},"4.049927","-1.31","3.63;3.63;.","0.999998;0.999998;0.999998;1","-2.34;-2.32;-2.34","0.98;.;.","0.009;0.012;0.008","0.941;0.858;0.93",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225314| C4225313","0/0","289,0","0","289","0/1","141,50","0.2618","191",null,"chr6:75175299:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2867"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","COL12A1","chr6:75175299","COL12A1(P817T)",null,null,"domain (Fibronectin type-III 5 ), splice variant (In isoform 2. )","domain:Fibronectin_type-III_5","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Ullrich congenital muscular dystrophy 2 (UCMD2) [MIM:616470]: A form of Ullrich muscular dystrophy, a congenital myopathy characterized by muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course is more severe than in Bethlem myopathy. {ECO:0000269|PubMed:24334604}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bethlem myopathy 2 (BTHLM2) [MIM:616471]: A form of Bethlem myopathy, a benign proximal myopathy characterized by early childhood onset and joint contractures most frequently affecting the elbows and ankles. BTHLM2 inheritance is autosomal dominant. {ECO:0000269|PubMed:24334604, ECO:0000269|PubMed:24334769}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type XII collagen interacts with type I collagen- containing fibrils, the COL1 domain could be associated with the surface of the fibrils, and the COL2 and NC3 domains may be localized in the perifibrillar matrix. {ECO:0000250}.; ",{"$nulls":4},"p.Pro817Thr","c.2449C>A","MODERATE","817/3063",13,{"$nulls":5},"5","291","252","206","174","284","235","0","0","0","0.2553",{"$nulls":20},"4.049927","-1.31","3.63;3.63;.","0.999998;0.999998;0.999998;1","-2.34;-2.32;-2.34","0.98;.;.","0.009;0.012;0.008","0.941;0.858;0.93",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225314| C4225313","0/0","289,0","0","289","0/1","179,66","0.2694","245",null,"chr6:75175299:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2759"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","CYTH1","chr17:78700373","CYTH1(Q170*)",null,null,"domain (SEC7 ), helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Promotes guanine-nucleotide exchange on ARF1, ARF5 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization, through regulation of ARF6 activity. {ECO:0000250|UniProtKB:Q9QX11, ECO:0000269|PubMed:10652308, ECO:0000269|PubMed:29420262, ECO:0000269|PubMed:9653114}.; ",{"$nulls":4},"p.Gln170*","c.508C>T","HIGH","170/398",7,{"$nulls":5},"5","651","781","455","567","558","656","0","0","0","0.1113",{"$nulls":5},"(CYTH1|ENSG00000108669|1|1.00)","(CYTH1|ENSG00000108669|1|1.00)",{"$nulls":13},"7.738397",null,null,"1",{"$nulls":3},"0.508;0.508;0.503;0.503;0.505;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the PSCD family. Members of this family have identical structural organization that consists of an N-terminal coiled-coil motif, a central Sec7 domain, and a C-terminal pleckstrin homology (PH) domain. The coiled-coil motif is involved in homodimerization, the Sec7 domain contains guanine-nucleotide exchange protein activity, and the PH domain interacts with phospholipids and is responsible for association of PSCDs with membranes. Members of this family appear to mediate the regulation of protein sorting and membrane trafficking. This gene is highly expressed in natural killer and peripheral T cells, and regulates the adhesiveness of integrins at the plasma membrane of lymphocytes. A pseudogene of this gene has been defined on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014].",null,null,"0/0","618,0","0","618","0/1","664,86","0.1147","750",null,"chr17:78700373:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1199"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","CYTH1","chr17:78700373","CYTH1(Q170*)",null,null,"domain (SEC7 ), helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Promotes guanine-nucleotide exchange on ARF1, ARF5 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization, through regulation of ARF6 activity. {ECO:0000250|UniProtKB:Q9QX11, ECO:0000269|PubMed:10652308, ECO:0000269|PubMed:29420262, ECO:0000269|PubMed:9653114}.; ",{"$nulls":4},"p.Gln170*","c.508C>T","HIGH","170/398",7,{"$nulls":5},"5","651","1035","455","735","559","904","0","0","0","0.1471",{"$nulls":5},"(CYTH1|ENSG00000108669|1|1.00)","(CYTH1|ENSG00000108669|1|1.00)",{"$nulls":13},"7.738397",null,null,"1",{"$nulls":3},"0.508;0.508;0.503;0.503;0.505;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the PSCD family. Members of this family have identical structural organization that consists of an N-terminal coiled-coil motif, a central Sec7 domain, and a C-terminal pleckstrin homology (PH) domain. The coiled-coil motif is involved in homodimerization, the Sec7 domain contains guanine-nucleotide exchange protein activity, and the PH domain interacts with phospholipids and is responsible for association of PSCDs with membranes. Members of this family appear to mediate the regulation of protein sorting and membrane trafficking. This gene is highly expressed in natural killer and peripheral T cells, and regulates the adhesiveness of integrins at the plasma membrane of lymphocytes. A pseudogene of this gene has been defined on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014].",null,null,"0/0","611,0","0","611","0/1","842,142","0.1443","984",null,"chr17:78700373:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1469"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","DACT2","chr6:168310198","DACT2(G210S)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in regulation of intracellular signaling pathways during development. Negatively regulates the Nodal signaling pathway, possibly by promoting the lysosomal degradation of Nodal receptors, such as TGFBR1. May be involved in control of the morphogenetic behavior of kidney ureteric bud cells by keeping cells epithelial and restraining their mesenchymal character. May play an inhibitory role in the re-epithelialization of skin wounds by attenuating TGF-beta signaling (By similarity). {ECO:0000250}.; ","mitocarta",{"$nulls":3},"p.Gly210Ser","c.628G>A","MODERATE","210/774",3,{"$nulls":5},"5","599","418","443","304","542","371","0","0","0","0.2453",{"$nulls":20},"0.54231","-1.62;0.31;.","1.895;1.895;.","1","-1.13;-1.36;.",".;0.949;.","0.066;0.256;.","0.11;0.097;0.086",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","598,0","0","598","0/1","300,113","0.2736","413",null,"chr6:168310198:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.273"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","DACT2","chr6:168310198","DACT2(G210S)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in regulation of intracellular signaling pathways during development. Negatively regulates the Nodal signaling pathway, possibly by promoting the lysosomal degradation of Nodal receptors, such as TGFBR1. May be involved in control of the morphogenetic behavior of kidney ureteric bud cells by keeping cells epithelial and restraining their mesenchymal character. May play an inhibitory role in the re-epithelialization of skin wounds by attenuating TGF-beta signaling (By similarity). {ECO:0000250}.; ","mitocarta",{"$nulls":3},"p.Gly210Ser","c.628G>A","MODERATE","210/774",3,{"$nulls":5},"5","599","495","443","369","543","425","0","0","0","0.2518",{"$nulls":20},"0.54231","-1.62;0.31;.","1.895;1.895;.","1","-1.13;-1.36;.",".;0.949;.","0.066;0.256;.","0.11;0.097;0.086",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","589,0","0","589","0/1","360,125","0.2577","485",null,"chr6:168310198:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2493"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","DCDC1","chr11:30906727","DCDC1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.3919-2A>C","HIGH",null,27,{"$nulls":5},"4","200","147","137","107","177","120","0.005","0.005","0","0.0583",{"$nulls":5},"(DCDC1|ENSG00000170959|1|1.00)",{"$nulls":14},"4.04053",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","201,1","0.005","202","0/1","131,14","0.0966","145",null,"chr11:30906727:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0841"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","DDX52","chr17:37632114","DDX52(H201R)",null,null,"domain (Helicase ATP-binding )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.His201Arg","c.602A>G","MODERATE","201/599",4,{"$nulls":5},"5","272","148","231","131","209","131","0","0","0","0.6107",{"$nulls":20},"2.909315",null,null,"0.999973;0.999955",{"$nulls":3},"0.764",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","269,0","0","269","0/1","61,87","0.5878","148",null,"chr17:37632114:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5954"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","DDX52","chr17:37632114","DDX52(H201R)",null,null,"domain (Helicase ATP-binding )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.His201Arg","c.602A>G","MODERATE","201/599",4,{"$nulls":5},"5","272","230","231","195","218","195","0","0","0","0.7333",{"$nulls":20},"2.909315",null,null,"0.999973;0.999955",{"$nulls":3},"0.764",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","263,0","0","263","0/1","70,157","0.6916","227",null,"chr17:37632114:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6821"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","DENND4B","chr1:153934764","DENND4B(Q923fs)",null,null,"compositionally biased region (Gln-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. {ECO:0000269|PubMed:20937701}.; ",{"$nulls":4},"p.Gln923fs","c.2768delA","HIGH","923/1496",18,{"$nulls":5},"4","514","521","329","327","268","282","0","0","0","0.156",{"$nulls":5},"(DENND4B|ENSG00000198837|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","464,0","0","464","0/1","381,84","0.1806","465",null,"chr1:153934764:CT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1743"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","DENND4B","chr1:153934764","DENND4B(Q923fs)",null,null,"compositionally biased region (Gln-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. {ECO:0000269|PubMed:20937701}.; ",{"$nulls":4},"p.Gln923fs","c.2768delA","HIGH","923/1496",18,{"$nulls":5},"4","514","601","329","399","269","319","0","0","0","0.1285",{"$nulls":5},"(DENND4B|ENSG00000198837|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","463,0","0","463","0/1","478,84","0.1495","562",null,"chr1:153934764:CT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1604"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","DNAH11","chr7:21801162","DNAH11(L3358R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Ciliary dyskinesia, primary, 7 (CILD7) [MIM:611884]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:12142464, ECO:0000269|PubMed:18022865, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.; ",{"$nulls":4},"p.Leu3358Arg","c.10073T>G","MODERATE","3358/4523",63,{"$nulls":5},"3",null,null,"89","74",{"$nulls":26},"3.948932",".;-1.53;.",null,"0.999988",".;-5.73;.",null,".;0.0;.","0.803;0.794;0.799",{"$nulls":3},"Unknown",-1,"AR","Ciliary dyskinesia, primary, 7","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary",{"$nulls":3},"C2678473","0/0","108,0","0","108","0/1","82,7","0.0787","89",null,"chr7:21801162:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1081"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","FAM189B","chr1:155250290","FAM189B(T499I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr499Ile","c.1496C>T","MODERATE","499/668",9,{"$nulls":5},"5","241","186","160","125","214","171","0","0","0","0.1637",{"$nulls":20},"2.037571","3.98",".;.;0.345","0.913846","-0.95;-0.74;-1.12","0.386;.;0.099","0.002","0.161;0.195;0.154",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","234,0","0","234","0/1","156,29","0.1568","185",null,"chr1:155250290:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.184"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","FAM189B","chr1:155250290","FAM189B(T499I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr499Ile","c.1496C>T","MODERATE","499/668",9,{"$nulls":5},"5","241","281","160","189","212","236","0","0","0","0.2203",{"$nulls":20},"2.037571","3.98",".;.;0.345","0.913846","-0.95;-0.74;-1.12","0.386;.;0.099","0.002","0.161;0.195;0.154",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","234,0","0","234","0/1","212,65","0.2347","277",null,"chr1:155250290:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2116"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","FOXG1","chr14:28767529","FOXG1(P84T)",null,null,"compositionally biased region (Pro-rich ), sequence conflict (In Ref. 1; CAA52240 and 2; CAA55038. ), sequence conflict (In Ref. 1; CAA52239. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription repression factor which plays an important role in the establishment of the regional subdivision of the developing brain and in the development of the telencephalon. {ECO:0000269|PubMed:12657635}.; ","epilepsy",{"$nulls":3},"p.Pro84Thr","c.250C>A","MODERATE","84/489",1,{"$nulls":5},"3","136","31","124","28",null,null,"0","0",{"$nulls":22},"1.639573","1.96","0.345","0.999826","-0.22","0.002","0.023","0.089",{"$nulls":3},"Unknown",-1,"AD","Rett syndrome, congenital variant","Neurologic",{"$nulls":3},"C3150705","0/0","135,0","0","135","0/1","25,6","0.1935","31",null,"chr14:28767529:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1786"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","FOXG1","chr14:28767529","FOXG1(P84T)",null,null,"compositionally biased region (Pro-rich ), sequence conflict (In Ref. 1; CAA52240 and 2; CAA55038. ), sequence conflict (In Ref. 1; CAA52239. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription repression factor which plays an important role in the establishment of the regional subdivision of the developing brain and in the development of the telencephalon. {ECO:0000269|PubMed:12657635}.; ","epilepsy",{"$nulls":3},"p.Pro84Thr","c.250C>A","MODERATE","84/489",1,{"$nulls":5},"3","136","59","124","51",null,null,"0","0",{"$nulls":22},"1.639573","1.96","0.345","0.999826","-0.22","0.002","0.023","0.089",{"$nulls":3},"Unknown",-1,"AD","Rett syndrome, congenital variant","Neurologic",{"$nulls":3},"C3150705","0/0","134,0","0","134","0/1","46,12","0.2069","58",null,"chr14:28767529:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2353"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","GNAL","chr18:11753871","GNAL(A184S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. G(olf) alpha mediates signal transduction within the olfactory neuroepithelium and the basal ganglia. May be involved in some aspect of visual transduction, and in mediating the effect of one or more hormones/neurotransmitters.; ",{"$nulls":4},"p.Ala184Ser","c.550G>T","MODERATE","184/458",4,{"$nulls":5},"4","768","716","550","497","665","642","0.0013","0.0013","0","0.1449",{"$nulls":20},"2.880079","1.01",".;1.255;1.255;1.255;.;.","1","-1.14;-1.14;-1.14;-1.14;.;.",".;0.085;0.085;0.085;.;.","0.169;0.363;0.363;0.363;.;.","0.431;0.418;0.418;0.418;.;.",{"$nulls":3},"Unknown",-1,"AD","Primary torsion dystonia","Neurologic",{"$nulls":3},"C3554447","0/0","727,1","0.0014","728","0/1","582,90","0.1339","672",null,"chr18:11753871:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1388"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","GNAL","chr18:11753871","GNAL(A184S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems. G(olf) alpha mediates signal transduction within the olfactory neuroepithelium and the basal ganglia. May be involved in some aspect of visual transduction, and in mediating the effect of one or more hormones/neurotransmitters.; ",{"$nulls":4},"p.Ala184Ser","c.550G>T","MODERATE","184/458",4,{"$nulls":5},"4","768","957","550","679","664","842","0.0013","0.0013","0","0.1295",{"$nulls":20},"2.880079","1.01",".;1.255;1.255;1.255;.;.","1","-1.14;-1.14;-1.14;-1.14;.;.",".;0.085;0.085;0.085;.;.","0.169;0.363;0.363;0.363;.;.","0.431;0.418;0.418;0.418;.;.",{"$nulls":3},"Unknown",-1,"AD","Primary torsion dystonia","Neurologic",{"$nulls":3},"C3554447","0/0","727,1","0.0014","728","0/1","778,115","0.1288","893",null,"chr18:11753871:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1267"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","GTDC1","chr2:143947060","GTDC1(D457Y)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp457Tyr","c.1369G>T","MODERATE","457/458",12,{"$nulls":5},"5","425","335","308","241","379","294","0","0","0","0.2007",{"$nulls":20},"3.908022","0.49;0.49;0.63;.;0.7;0.49;0.49;0.39","1.87;1.87;.;.;.;1.87;1.87;.","0.999997;0.999997;0.899175;0.991892;0.999997;0.999997;0.899175;0.999997","-2.69;-2.69;-2.38;.;-2.75;-2.69;-2.69;-2.64","0.998;0.998;0.999;.;0.881;0.998;0.998;.","0.0;0.0;0.0;.;0.0;0.0;0.0;0.0","0.509;0.548;0.476;0.506;0.487;0.543;0.543;0.56",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","393,0","0","393","0/1","259,65","0.2006","324",null,"chr2:143947060:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2116"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","GUCY2F","chrX:109398591","GUCY2F(V745F)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably plays a specific functional role in the rods and/or cones of photoreceptors. It may be the enzyme involved in the resynthesis of cGMP required for recovery of the dark state after phototransduction.; ",{"$nulls":4},"p.Val745Phe","c.2233G>T","MODERATE","745/1108",11,{"$nulls":5},"5","263","277","212","219","200","222","0","0","0","0.1396",{"$nulls":20},"1.938276","0.03","0.925","0.993582","-2.61","0.009","0.011","0.631",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","253,0","0","253","0/1","231,30","0.1149","261",null,"chrX:109398591:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1324"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","GUCY2F","chrX:109398591","GUCY2F(V745F)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably plays a specific functional role in the rods and/or cones of photoreceptors. It may be the enzyme involved in the resynthesis of cGMP required for recovery of the dark state after phototransduction.; ",{"$nulls":4},"p.Val745Phe","c.2233G>T","MODERATE","745/1108",11,{"$nulls":5},"5","263","236","212","186","197","194","0","0","0","0.268",{"$nulls":20},"1.938276","0.03","0.925","0.993582","-2.61","0.009","0.011","0.631",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","253,0","0","253","0/1","169,57","0.2522","226",null,"chrX:109398591:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2419"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","HLA-DOB","chr6:32815305","HLA-DOB(V34L)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule in B-cells. Modifies peptide exchange activity of HLA-DM.; ",{"$nulls":4},"p.Val34Leu","c.100G>T","MODERATE","34/273",2,{"$nulls":5},"5","232","264","160","176","222","250","0","0","0","0.056",{"$nulls":20},"1.504723","2.13;.","1.56","1","-0.27;.","0.168","0.737;.","0.421;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","228,0","0","228","0/1","245,15","0.0577","260",null,"chr6:32815305:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","HSF5","chr17:58422413","HSF5(D580H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a transcriptional factor. {ECO:0000250}.; ",{"$nulls":4},"p.Asp580His","c.1738G>C","MODERATE","580/596",6,{"$nulls":5},"5","466","443","315","299","420","385","0","0","0","0.3273",{"$nulls":20},"3.842357","-0.85",null,"0.994089","-1.3",null,null,"0.747",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","431,0","0","431","0/1","281,150","0.348","431",null,"chr17:58422413:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3278"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","HSF5","chr17:58422413","HSF5(D580H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a transcriptional factor. {ECO:0000250}.; ",{"$nulls":4},"p.Asp580His","c.1738G>C","MODERATE","580/596",6,{"$nulls":5},"5","466","567","315","379","422","493","0","0","0","0.355",{"$nulls":20},"3.842357","-0.85",null,"0.994089","-1.3",null,null,"0.747",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","430,0","0","430","0/1","331,193","0.3683","524",null,"chr17:58422413:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3588"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","IRX6","chr16:55328724","IRX6(R249L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg249Leu","c.746G>T","MODERATE","249/446",5,{"$nulls":5},"5","285","443","221","330","193","335","0","0","0","0.0687",{"$nulls":20},"2.426703","-2.53","1.79","0.756008","-2.12","0.532","0.016","0.217",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","278,0","0","278","0/1","399,28","0.0656","427",null,"chr16:55328724:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0636"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","KATNB1","chr16:57741777","KATNB1(V45fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lissencephaly 6, with microcephaly (LIS6) [MIM:616212]: A form of lissencephaly, a disorder of cortical development characterized by agyria or pachygyria and disorganization of the clear neuronal lamination of normal six-layered cortex. LIS6 features include hypoplasia of the corpus callosum, severe microcephaly and developmental delay. {ECO:0000269|PubMed:25521378, ECO:0000269|PubMed:25521379}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation. Microtubule release from the mitotic spindle poles may allow depolymerization of the microtubule end proximal to the spindle pole, leading to poleward microtubule flux and poleward motion of chromosome. Microtubule release within the cell body of neurons may be required for their transport into neuronal processes by microtubule-dependent motor proteins. This transport is required for axonal growth. {ECO:0000255|HAMAP-Rule:MF_03022, ECO:0000269|PubMed:10751153}.; ",{"$nulls":4},"p.Val45fs","c.132delC","HIGH","44/655",3,{"$nulls":5},"4","499","450","319","297","428","376","0","0","0","0.1835",{"$nulls":5},"(KATNB1|ENSG00000140854|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Lissencephaly 6, with microcephaly","Neurologic",{"$nulls":3},"C4015525","0/0","464,0","0","464","0/1","330,89","0.2124","419",null,"chr16:57741777:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1919"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","KATNB1","chr16:57741777","KATNB1(V45fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lissencephaly 6, with microcephaly (LIS6) [MIM:616212]: A form of lissencephaly, a disorder of cortical development characterized by agyria or pachygyria and disorganization of the clear neuronal lamination of normal six-layered cortex. LIS6 features include hypoplasia of the corpus callosum, severe microcephaly and developmental delay. {ECO:0000269|PubMed:25521378, ECO:0000269|PubMed:25521379}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Participates in a complex which severs microtubules in an ATP-dependent manner. May act to target the enzymatic subunit of this complex to sites of action such as the centrosome. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation. Microtubule release from the mitotic spindle poles may allow depolymerization of the microtubule end proximal to the spindle pole, leading to poleward microtubule flux and poleward motion of chromosome. Microtubule release within the cell body of neurons may be required for their transport into neuronal processes by microtubule-dependent motor proteins. This transport is required for axonal growth. {ECO:0000255|HAMAP-Rule:MF_03022, ECO:0000269|PubMed:10751153}.; ",{"$nulls":4},"p.Val45fs","c.132delC","HIGH","44/655",3,{"$nulls":5},"4","499","523","319","348","428","445","0","0","0","0.2157",{"$nulls":5},"(KATNB1|ENSG00000140854|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Lissencephaly 6, with microcephaly","Neurologic",{"$nulls":3},"C4015525","0/0","464,0","0","464","0/1","375,115","0.2347","490",null,"chr16:57741777:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.204"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","KCND3","chr1:111982375","KCND3(L118M)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia 19 (SCA19) [MIM:607346]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA19 is a relatively mild, cerebellar ataxic syndrome with cognitive impairment, pyramidal tract involvement, tremor and peripheral neuropathy, and mild atrophy of the cerebellar hemispheres and vermis. {ECO:0000269|PubMed:23280837, ECO:0000269|PubMed:23280838, ECO:0000269|PubMed:28895081}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brugada syndrome 9 (BRGDA9) [MIM:616399]: A tachyarrhythmia characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will faint and may die in a few minutes if the heart is not reset. {ECO:0000269|PubMed:21349352, ECO:0000269|PubMed:22457051}. Note=The gene represented in this entry may be involved in disease pathogenesis.; ","FUNCTION: Pore-forming (alpha) subunit of voltage-gated rapidly inactivating A-type potassium channels. May contribute to I(To) current in heart and I(Sa) current in neurons. Channel properties are modulated by interactions with other alpha subunits and with regulatory subunits. {ECO:0000269|PubMed:10200233, ECO:0000269|PubMed:9843794}.; ",{"$nulls":4},"p.Leu118Met","c.352C>A","MODERATE","118/655",2,{"$nulls":5},"4","908","808","688","625","757","666","0.0011","0.0011","0","0.3273",{"$nulls":20},"3.5218059999999998","0.81","2.54","1","-1.77;-1.84;-1.77",".;1.0;.","0.002;0.001;0.002","0.737;0.593;0.737",{"$nulls":3},"Unknown",-1,"AD","Spinocerebellar ataxia 19; Spinocerebellar ataxia 22","Neurologic",{"$nulls":3},"C1846367| C4225340","0/0","877,0","0","877","0/1","539,256","0.322","795",null,"chr1:111982375:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3328"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","KCND3","chr1:111982375","KCND3(L118M)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spinocerebellar ataxia 19 (SCA19) [MIM:607346]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA19 is a relatively mild, cerebellar ataxic syndrome with cognitive impairment, pyramidal tract involvement, tremor and peripheral neuropathy, and mild atrophy of the cerebellar hemispheres and vermis. {ECO:0000269|PubMed:23280837, ECO:0000269|PubMed:23280838, ECO:0000269|PubMed:28895081}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brugada syndrome 9 (BRGDA9) [MIM:616399]: A tachyarrhythmia characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will faint and may die in a few minutes if the heart is not reset. {ECO:0000269|PubMed:21349352, ECO:0000269|PubMed:22457051}. Note=The gene represented in this entry may be involved in disease pathogenesis.; ","FUNCTION: Pore-forming (alpha) subunit of voltage-gated rapidly inactivating A-type potassium channels. May contribute to I(To) current in heart and I(Sa) current in neurons. Channel properties are modulated by interactions with other alpha subunits and with regulatory subunits. {ECO:0000269|PubMed:10200233, ECO:0000269|PubMed:9843794}.; ",{"$nulls":4},"p.Leu118Met","c.352C>A","MODERATE","118/655",2,{"$nulls":5},"4","908","1032","688","800","758","865","0.0011","0.0011","0","0.3942",{"$nulls":20},"3.5218059999999998","0.81","2.54","1","-1.77;-1.84;-1.77",".;1.0;.","0.002;0.001;0.002","0.737;0.593;0.737",{"$nulls":3},"Unknown",-1,"AD","Spinocerebellar ataxia 19; Spinocerebellar ataxia 22","Neurologic",{"$nulls":3},"C1846367| C4225340","0/0","876,0","0","876","0/1","619,395","0.3895","1014",null,"chr1:111982375:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3862"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","KPRP","chr1:152759927","KPRP(C113*)",null,null,"compositionally biased region (Gln-rich ), sequence variant (In dbSNP:rs16834457. KPRP(C113R))",{"$nulls":3},255,"PASS","Loss Of Function","rs751837891",8.637e-05,{"$nulls":6},"p.Cys113*","c.339C>A","HIGH","113/579",1,{"$nulls":5},"4","592","463","454","373","390","312","0","0","0","0.6859",{"$nulls":20},"5.435362",null,null,"1",{"$nulls":3},"0.136",{"$nulls":3},"ExAC_AMR_AF",8.637e-05,{"$nulls":7},"0/0","582,1","0.0017","583","0/1","151,301","0.6659","452",null,"chr1:152759927:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6622"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","KPRP","chr1:152759927","KPRP(C113*)",null,null,"compositionally biased region (Gln-rich ), sequence variant (In dbSNP:rs16834457. KPRP(C113R))",{"$nulls":3},255,"PASS","Loss Of Function","rs751837891",8.637e-05,{"$nulls":6},"p.Cys113*","c.339C>A","HIGH","113/579",1,{"$nulls":5},"4","592","542","454","410","389","375","0","0","0","0.744",{"$nulls":20},"5.435362",null,null,"1",{"$nulls":3},"0.136",{"$nulls":3},"ExAC_AMR_AF",8.637e-05,{"$nulls":7},"0/0","579,1","0.0017","580","0/1","156,381","0.7095","537",null,"chr1:152759927:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6976"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LAMB2","chr3:49122893","LAMB2(E1462Q)",null,null,"region of interest (Domain I )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Pierson syndrome (PIERSS) [MIM:609049]: Characterized by nephrotic syndrome with neonatal onset, diffuse mesangial sclerosis and eye abnormalities with microcoria as the leading clinical feature. Death usually occurs within the first weeks of life. Disease severity depends on the mutation type: nontruncating LAMB2 mutations may display variable phenotypes ranging from a milder variant of Pierson syndrome to isolated congenital nephrotic syndrome. {ECO:0000269|PubMed:15367484, ECO:0000269|PubMed:16912710}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Nephrotic syndrome 5 with or without ocular abnormalities (NPHS5) [MIM:614199]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. NPHS5 is characterized by very early onset of progressive renal failure. A subset of patients may develop mild ocular anomalies, such as myopia, nystagmus, and strabismus. {ECO:0000269|PubMed:20798252, ECO:0000269|PubMed:21236492}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.; ","level2",{"$nulls":3},"p.Glu1462Gln","c.4384G>C","MODERATE","1462/1798",27,{"$nulls":5},"5","834","813","599","582","711","707","0","0","0","0.1641",{"$nulls":20},"3.202295","1.34","2.055","1","-1.55","1.0","0.173","0.326;0.324",{"$nulls":3},"Unknown",-1,"AR","Pierson syndrome; Nephrotic syndrome, type 5, with or without ocular abnormalities","Musculoskeletal; Neurologic; Ophthalmologic; Renal","kCANCER",null,null,"C1836876| C3280113","0/0","797,0","0","797","0/1","655,133","0.1688","788",null,"chr3:49122893:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1684"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LAMB2","chr3:49122893","LAMB2(E1462Q)",null,null,"region of interest (Domain I )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Pierson syndrome (PIERSS) [MIM:609049]: Characterized by nephrotic syndrome with neonatal onset, diffuse mesangial sclerosis and eye abnormalities with microcoria as the leading clinical feature. Death usually occurs within the first weeks of life. Disease severity depends on the mutation type: nontruncating LAMB2 mutations may display variable phenotypes ranging from a milder variant of Pierson syndrome to isolated congenital nephrotic syndrome. {ECO:0000269|PubMed:15367484, ECO:0000269|PubMed:16912710}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Nephrotic syndrome 5 with or without ocular abnormalities (NPHS5) [MIM:614199]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. NPHS5 is characterized by very early onset of progressive renal failure. A subset of patients may develop mild ocular anomalies, such as myopia, nystagmus, and strabismus. {ECO:0000269|PubMed:20798252, ECO:0000269|PubMed:21236492}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.; ","level2",{"$nulls":3},"p.Glu1462Gln","c.4384G>C","MODERATE","1462/1798",27,{"$nulls":5},"5","834","889","599","653","713","779","0","0","0","0.2362",{"$nulls":20},"3.202295","1.34","2.055","1","-1.55","1.0","0.173","0.326;0.324",{"$nulls":3},"Unknown",-1,"AR","Pierson syndrome; Nephrotic syndrome, type 5, with or without ocular abnormalities","Musculoskeletal; Neurologic; Ophthalmologic; Renal","kCANCER",null,null,"C1836876| C3280113","0/0","799,0","0","799","0/1","650,203","0.238","853",null,"chr3:49122893:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2343"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LBR","chr1:225403461","LBR(G563fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pelger-Huet anomaly (PHA) [MIM:169400]: An autosomal dominant inherited abnormality of granulocytes, characterized by abnormal ovoid shape, reduced nuclear segmentation and an apparently looser chromatin structure. {ECO:0000269|PubMed:14617022}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Greenberg dysplasia (GRBGD) [MIM:215140]: A rare autosomal recessive chondrodystrophy characterized by early in utero lethality. Affected fetuses typically present with fetal hydrops, short-limbed dwarfism, and a marked disorganization of chondro-osseous calcification, and ectopic ossification centers. {ECO:0000269|PubMed:12618959}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reynolds syndrome (REYNS) [MIM:613471]: A syndrome specifically associating limited cutaneous systemic sclerosis and primary biliary cirrhosis. It is characterized by liver disease, telangiectasia, abrupt onset of digital paleness or cyanosis in response to cold exposure or stress (Raynaud phenomenon), and variable features of scleroderma. The liver disease is characterized by pruritis, jaundice, hepatomegaly, increased serum alkaline phosphatase and positive serum mitochondrial autoantibodies, all consistent with primary biliary cirrhosis. {ECO:0000269|PubMed:20522425}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Anchors the lamina and the heterochromatin to the inner nuclear membrane. {ECO:0000269|PubMed:10828963}.; ",{"$nulls":4},"p.Gly563fs","c.1688-9_1690del>GAN_EAELED<insT","HIGH","563/615",14,{"$nulls":20},"225404401",{"$nulls":26},"Unknown",-1,"AD","Hydrops-ectopic calcification-moth-eaten skeletal dysplasia; Reynolds syndrome; Pelger-Huet anomaly; Greenberg/HEM skeletal dysplasia","Craniofacial; Hematologic; Musculoskeletal",{"$nulls":3},"C2931048| C0030779| C4747922| C0748397",{"$nulls":9},"chr1:225403461:<DELETE_NUC>:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LBR","chr1:225403461","LBR(G563fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pelger-Huet anomaly (PHA) [MIM:169400]: An autosomal dominant inherited abnormality of granulocytes, characterized by abnormal ovoid shape, reduced nuclear segmentation and an apparently looser chromatin structure. {ECO:0000269|PubMed:14617022}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Greenberg dysplasia (GRBGD) [MIM:215140]: A rare autosomal recessive chondrodystrophy characterized by early in utero lethality. Affected fetuses typically present with fetal hydrops, short-limbed dwarfism, and a marked disorganization of chondro-osseous calcification, and ectopic ossification centers. {ECO:0000269|PubMed:12618959}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reynolds syndrome (REYNS) [MIM:613471]: A syndrome specifically associating limited cutaneous systemic sclerosis and primary biliary cirrhosis. It is characterized by liver disease, telangiectasia, abrupt onset of digital paleness or cyanosis in response to cold exposure or stress (Raynaud phenomenon), and variable features of scleroderma. The liver disease is characterized by pruritis, jaundice, hepatomegaly, increased serum alkaline phosphatase and positive serum mitochondrial autoantibodies, all consistent with primary biliary cirrhosis. {ECO:0000269|PubMed:20522425}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Anchors the lamina and the heterochromatin to the inner nuclear membrane. {ECO:0000269|PubMed:10828963}.; ",{"$nulls":4},"p.Gly563fs","c.1688-9_1690del>GAN_EAELED<insT","HIGH","563/615",14,{"$nulls":20},"225404401",{"$nulls":26},"Unknown",-1,"AD","Hydrops-ectopic calcification-moth-eaten skeletal dysplasia; Reynolds syndrome; Pelger-Huet anomaly; Greenberg/HEM skeletal dysplasia","Craniofacial; Hematologic; Musculoskeletal",{"$nulls":3},"C2931048| C0030779| C4747922| C0748397",{"$nulls":9},"chr1:225403461:<DELETE_NUC>:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LBR","chr1:225404526","LBR(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Pelger-Huet anomaly (PHA) [MIM:169400]: An autosomal dominant inherited abnormality of granulocytes, characterized by abnormal ovoid shape, reduced nuclear segmentation and an apparently looser chromatin structure. {ECO:0000269|PubMed:14617022}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Greenberg dysplasia (GRBGD) [MIM:215140]: A rare autosomal recessive chondrodystrophy characterized by early in utero lethality. Affected fetuses typically present with fetal hydrops, short-limbed dwarfism, and a marked disorganization of chondro-osseous calcification, and ectopic ossification centers. {ECO:0000269|PubMed:12618959}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reynolds syndrome (REYNS) [MIM:613471]: A syndrome specifically associating limited cutaneous systemic sclerosis and primary biliary cirrhosis. It is characterized by liver disease, telangiectasia, abrupt onset of digital paleness or cyanosis in response to cold exposure or stress (Raynaud phenomenon), and variable features of scleroderma. The liver disease is characterized by pruritis, jaundice, hepatomegaly, increased serum alkaline phosphatase and positive serum mitochondrial autoantibodies, all consistent with primary biliary cirrhosis. {ECO:0000269|PubMed:20522425}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Anchors the lamina and the heterochromatin to the inner nuclear membrane. {ECO:0000269|PubMed:10828963}.; ",{"$nulls":5},"c.1564+1_1565-1delGTAAGTATTGATTTATGTTTATATTATATATATTACATGAAGGTTTTATTTTTCTTTTTGTCTCGACATCATTAAAAATGTACTTTTATTTTTATATAG","HIGH",null,12,{"$nulls":20},"225404625",{"$nulls":26},"Unknown",-1,"AD","Hydrops-ectopic calcification-moth-eaten skeletal dysplasia; Reynolds syndrome; Pelger-Huet anomaly; Greenberg/HEM skeletal dysplasia","Craniofacial; Hematologic; Musculoskeletal",{"$nulls":3},"C2931048| C0030779| C4747922| C0748397",{"$nulls":9},"chr1:225404526:TCTATATAAAAATAAAAGTACATTTTTAATGATGTCGAGACAAAAAGAAAAATAAAACCTTCATGTAATATATATAATATAAACATAAATCAATACTTAC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LBR","chr1:225404526","LBR(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Pelger-Huet anomaly (PHA) [MIM:169400]: An autosomal dominant inherited abnormality of granulocytes, characterized by abnormal ovoid shape, reduced nuclear segmentation and an apparently looser chromatin structure. {ECO:0000269|PubMed:14617022}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Greenberg dysplasia (GRBGD) [MIM:215140]: A rare autosomal recessive chondrodystrophy characterized by early in utero lethality. Affected fetuses typically present with fetal hydrops, short-limbed dwarfism, and a marked disorganization of chondro-osseous calcification, and ectopic ossification centers. {ECO:0000269|PubMed:12618959}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reynolds syndrome (REYNS) [MIM:613471]: A syndrome specifically associating limited cutaneous systemic sclerosis and primary biliary cirrhosis. It is characterized by liver disease, telangiectasia, abrupt onset of digital paleness or cyanosis in response to cold exposure or stress (Raynaud phenomenon), and variable features of scleroderma. The liver disease is characterized by pruritis, jaundice, hepatomegaly, increased serum alkaline phosphatase and positive serum mitochondrial autoantibodies, all consistent with primary biliary cirrhosis. {ECO:0000269|PubMed:20522425}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Anchors the lamina and the heterochromatin to the inner nuclear membrane. {ECO:0000269|PubMed:10828963}.; ",{"$nulls":5},"c.1564+1_1565-1delGTAAGTATTGATTTATGTTTATATTATATATATTACATGAAGGTTTTATTTTTCTTTTTGTCTCGACATCATTAAAAATGTACTTTTATTTTTATATAG","HIGH",null,12,{"$nulls":20},"225404625",{"$nulls":26},"Unknown",-1,"AD","Hydrops-ectopic calcification-moth-eaten skeletal dysplasia; Reynolds syndrome; Pelger-Huet anomaly; Greenberg/HEM skeletal dysplasia","Craniofacial; Hematologic; Musculoskeletal",{"$nulls":3},"C2931048| C0030779| C4747922| C0748397",{"$nulls":9},"chr1:225404526:TCTATATAAAAATAAAAGTACATTTTTAATGATGTCGAGACAAAAAGAAAAATAAAACCTTCATGTAATATATATAATATAAACATAAATCAATACTTAC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LBR","chr1:225410414","LBR(V397fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pelger-Huet anomaly (PHA) [MIM:169400]: An autosomal dominant inherited abnormality of granulocytes, characterized by abnormal ovoid shape, reduced nuclear segmentation and an apparently looser chromatin structure. {ECO:0000269|PubMed:14617022}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Greenberg dysplasia (GRBGD) [MIM:215140]: A rare autosomal recessive chondrodystrophy characterized by early in utero lethality. Affected fetuses typically present with fetal hydrops, short-limbed dwarfism, and a marked disorganization of chondro-osseous calcification, and ectopic ossification centers. {ECO:0000269|PubMed:12618959}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reynolds syndrome (REYNS) [MIM:613471]: A syndrome specifically associating limited cutaneous systemic sclerosis and primary biliary cirrhosis. It is characterized by liver disease, telangiectasia, abrupt onset of digital paleness or cyanosis in response to cold exposure or stress (Raynaud phenomenon), and variable features of scleroderma. The liver disease is characterized by pruritis, jaundice, hepatomegaly, increased serum alkaline phosphatase and positive serum mitochondrial autoantibodies, all consistent with primary biliary cirrhosis. {ECO:0000269|PubMed:20522425}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Anchors the lamina and the heterochromatin to the inner nuclear membrane. {ECO:0000269|PubMed:10828963}.; ",{"$nulls":4},"p.Val397fs","c.1189-9_1191del>GAN_EAELED<insG","HIGH","397/615",10,{"$nulls":20},"225411334",{"$nulls":26},"Unknown",-1,"AD","Hydrops-ectopic calcification-moth-eaten skeletal dysplasia; Reynolds syndrome; Pelger-Huet anomaly; Greenberg/HEM skeletal dysplasia","Craniofacial; Hematologic; Musculoskeletal",{"$nulls":3},"C2931048| C0030779| C4747922| C0748397",{"$nulls":9},"chr1:225410414:<DELETE_NUC>:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LBR","chr1:225410414","LBR(V397fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pelger-Huet anomaly (PHA) [MIM:169400]: An autosomal dominant inherited abnormality of granulocytes, characterized by abnormal ovoid shape, reduced nuclear segmentation and an apparently looser chromatin structure. {ECO:0000269|PubMed:14617022}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Greenberg dysplasia (GRBGD) [MIM:215140]: A rare autosomal recessive chondrodystrophy characterized by early in utero lethality. Affected fetuses typically present with fetal hydrops, short-limbed dwarfism, and a marked disorganization of chondro-osseous calcification, and ectopic ossification centers. {ECO:0000269|PubMed:12618959}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Reynolds syndrome (REYNS) [MIM:613471]: A syndrome specifically associating limited cutaneous systemic sclerosis and primary biliary cirrhosis. It is characterized by liver disease, telangiectasia, abrupt onset of digital paleness or cyanosis in response to cold exposure or stress (Raynaud phenomenon), and variable features of scleroderma. The liver disease is characterized by pruritis, jaundice, hepatomegaly, increased serum alkaline phosphatase and positive serum mitochondrial autoantibodies, all consistent with primary biliary cirrhosis. {ECO:0000269|PubMed:20522425}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Anchors the lamina and the heterochromatin to the inner nuclear membrane. {ECO:0000269|PubMed:10828963}.; ",{"$nulls":4},"p.Val397fs","c.1189-9_1191del>GAN_EAELED<insG","HIGH","397/615",10,{"$nulls":20},"225411334",{"$nulls":26},"Unknown",-1,"AD","Hydrops-ectopic calcification-moth-eaten skeletal dysplasia; Reynolds syndrome; Pelger-Huet anomaly; Greenberg/HEM skeletal dysplasia","Craniofacial; Hematologic; Musculoskeletal",{"$nulls":3},"C2931048| C0030779| C4747922| C0748397",{"$nulls":9},"chr1:225410414:<DELETE_NUC>:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LDLRAD3","chr11:35944114","LDLRAD3(P6S)",null,null,"signal peptide ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May influence APP processing, resulting in a decrease in sAPP-alpha production and increased amyloidogenic P3 peptide production. {ECO:0000250}.; ",{"$nulls":4},"p.Pro6Ser","c.16C>T","MODERATE","6/345",1,{"$nulls":5},"4","71","45","47","33","58","35","0","0","0","0.3714",{"$nulls":20},"2.731881","-3.25;-3.1;-3.02","0.55;.;0.55","0.980524","-0.4;-0.78;-0.01",".;.;0.909","0.0;0.0;0.327","0.075;0.107;0.158",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","67,0","0","67","0/1","27,18","0.4","45",null,"chr11:35944114:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3939"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LDLRAD3","chr11:35944114","LDLRAD3(P6S)",null,null,"signal peptide ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May influence APP processing, resulting in a decrease in sAPP-alpha production and increased amyloidogenic P3 peptide production. {ECO:0000250}.; ",{"$nulls":4},"p.Pro6Ser","c.16C>T","MODERATE","6/345",1,{"$nulls":5},"4","71","63","47","42","57","48","0","0","0","0.1458",{"$nulls":20},"2.731881","-3.25;-3.1;-3.02","0.55;.;0.55","0.980524","-0.4;-0.78;-0.01",".;.;0.909","0.0;0.0;0.327","0.075;0.107;0.158",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","67,0","0","67","0/1","50,13","0.2063","63",null,"chr11:35944114:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2143"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LRRN1","chr3:3846641","LRRN1(K667T)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys667Thr","c.2000A>C","MODERATE","667/716",2,{"$nulls":5},"5","305","210","223","163","259","179","0","0","0","0.2291",{"$nulls":20},"3.494949","0.55","2.175","1;0.999995","-1.11","0.999","0.014","0.7",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","301,0","0","301","0/1","162,47","0.2249","209",null,"chr3:3846641:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2147"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LRRN1","chr3:3846641","LRRN1(K667T)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys667Thr","c.2000A>C","MODERATE","667/716",2,{"$nulls":5},"5","305","268","223","188","258","230","0","0","0","0.1217",{"$nulls":20},"3.494949","0.55","2.175","1;0.999995","-1.11","0.999","0.014","0.7",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","301,0","0","301","0/1","232,30","0.1145","262",null,"chr3:3846641:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1117"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","LTN1","chr21:28992847","LTN1(N33H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23685075, PubMed:25132172, PubMed:25578875). Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product (By similarity). {ECO:0000250|UniProtKB:Q04781, ECO:0000269|PubMed:23685075, ECO:0000269|PubMed:25132172, ECO:0000269|PubMed:25578875}.; ",{"$nulls":4},"p.Asn33His","c.97A>C","MODERATE","33/1812",1,{"$nulls":5},"5","1246","1018","845","700","1095","889","0","0","0","0.3982",{"$nulls":20},"1.557369","2.26;.;1.9",null,"1;0.999617;0.999617","0.02;.;-0.15",null,"0.098;.;0.056","0.166;0.191;0.227",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1177,0","0","1177","0/1","594,377","0.3883","971",null,"chr21:28992847:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3771"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","LTN1","chr21:28992847","LTN1(N33H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23685075, PubMed:25132172, PubMed:25578875). Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product (By similarity). {ECO:0000250|UniProtKB:Q04781, ECO:0000269|PubMed:23685075, ECO:0000269|PubMed:25132172, ECO:0000269|PubMed:25578875}.; ",{"$nulls":4},"p.Asn33His","c.97A>C","MODERATE","33/1812",1,{"$nulls":5},"5","1246","1290","845","883","1092","1110","0","0","0","0.4811",{"$nulls":20},"1.557369","2.26;.;1.9",null,"1;0.999617;0.999617","0.02;.;-0.15",null,"0.098;.;0.056","0.166;0.191;0.227",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1166,0","0","1166","0/1","623,601","0.491","1224",null,"chr21:28992847:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4632"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MRC2","chr17:62680803","MRC2(R826Q)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs555402959",0.002399,null,"FUNCTION: May play a role as endocytotic lectin receptor displaying calcium-dependent lectin activity. Internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. May be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. May contribute to cellular uptake, remodeling and degradation of extracellular collagen matrices. May play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. May participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). {ECO:0000269|PubMed:10683150, ECO:0000269|PubMed:12972549}.; ",{"$nulls":4},"p.Arg826Gln","c.2477G>A","MODERATE","826/1479",17,1,{"$nulls":4},"5","484","473","399","397","376","371","0","0","0","0.3504",{"$nulls":20},"2.272597","3.45","1.1","0.762237","0.1","0.001","0.381","0.319",{"$nulls":3},"ExAC_SAS_AF",0.002399,{"$nulls":7},"0/0","481,0","0","481","0/1","318,141","0.3072","459",null,"chr17:62680803:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2972"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","MRC2","chr17:62680803","MRC2(R826Q)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs555402959",0.002399,null,"FUNCTION: May play a role as endocytotic lectin receptor displaying calcium-dependent lectin activity. Internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. May be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. May contribute to cellular uptake, remodeling and degradation of extracellular collagen matrices. May play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. May participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). {ECO:0000269|PubMed:10683150, ECO:0000269|PubMed:12972549}.; ",{"$nulls":4},"p.Arg826Gln","c.2477G>A","MODERATE","826/1479",17,1,{"$nulls":4},"5","484","600","399","498","375","466","0","0","0","0.3112",{"$nulls":20},"2.272597","3.45","1.1","0.762237","0.1","0.001","0.381","0.319",{"$nulls":3},"ExAC_SAS_AF",0.002399,{"$nulls":7},"0/0","481,0","0","481","0/1","409,181","0.3068","590",null,"chr17:62680803:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3092"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MRC2","chr17:62681916","MRC2(V928M)",null,null,"topological domain (Extracellular ), domain (C-type lectin 5 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role as endocytotic lectin receptor displaying calcium-dependent lectin activity. Internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. May be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. May contribute to cellular uptake, remodeling and degradation of extracellular collagen matrices. May play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. May participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). {ECO:0000269|PubMed:10683150, ECO:0000269|PubMed:12972549}.; ",{"$nulls":4},"p.Val928Met","c.2782G>A","MODERATE","928/1479",19,{"$nulls":5},"5","375","405","259","282","333","354","0","0","0","0.3023",{"$nulls":20},"4.215333","1.92","3.085","1","-2.14","1.0","0.096","0.533",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","367,0","0","367","0/1","273,119","0.3036","392",null,"chr17:62681916:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3014"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","MRC2","chr17:62681916","MRC2(V928M)",null,null,"topological domain (Extracellular ), domain (C-type lectin 5 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role as endocytotic lectin receptor displaying calcium-dependent lectin activity. Internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. May be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. May contribute to cellular uptake, remodeling and degradation of extracellular collagen matrices. May play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. May participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). {ECO:0000269|PubMed:10683150, ECO:0000269|PubMed:12972549}.; ",{"$nulls":4},"p.Val928Met","c.2782G>A","MODERATE","928/1479",19,{"$nulls":5},"5","375","549","259","374","335","487","0","0","0","0.4271",{"$nulls":20},"4.215333","1.92","3.085","1","-2.14","1.0","0.096","0.533",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","367,0","0","367","0/1","307,233","0.4315","540",null,"chr17:62681916:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4091"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MROH2B","chr5:41008666","MROH2B(W1183L)",null,null,"repeat (HEAT 13 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the process of sperm capacitation. {ECO:0000250|UniProtKB:Q7M6Y6}.; ","tcga-gbm",{"$nulls":3},"p.Trp1183Leu","c.3548G>T","MODERATE","1183/1585",33,{"$nulls":5},"5","347","269","250","195","299","223","0","0","0","0.1839",{"$nulls":20},"-0.500194","5.09;5.34",".;-0.51","1","0.69;0.39",".;0.0","0.927;1.0","0.167;0.174",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","331,0","0","331","0/1","217,42","0.1622","259",null,"chr5:41008666:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1641"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MRPS25","chr3:15052527","MRPS25(Q146E)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Gln146Glu","c.436C>G","MODERATE","146/173",4,{"$nulls":5},"4","432","322","308","220","363","251","0","0","0","0.0598",{"$nulls":20},"3.913851",null,"2.98","1","-2.89","0.997",null,"0.737",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","401,0","0","401","0/1","290,17","0.0554","307",null,"chr3:15052527:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0636"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MUC3A","chr7:100964811","MUC3A(Splicing Altered)",null,null,"domain (SEA ), splice variant (In isoform 2. ), splice variant (In isoform 3. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Splicing Altered",null,-1,null,"FUNCTION: Major glycoprotein component of a variety of mucus gels. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. May be involved in ligand binding and intracellular signaling. {ECO:0000269|PubMed:10405327}.; ",{"$nulls":4},"p.Asp3119_Gln3127del","c.9355_9381delGATGTGAACAGCTGCCAGGACTCCCAG","MODERATE","3119/3323",6,{"$nulls":5},"4","476","488","331","345","256","260","0","0","0","0.1154",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","508,0","0","508","0/1","467,38","0.0752","505",null,"chr7:100964811:GCCAGGATGTGAACAGCTGCCAGGACTC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0928"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MUC5AC","chr11:1185126","MUC5AC(P2328fs)",null,null,"region of interest (9 X Cys-rich subdomain repeats ), region of interest (107 X 8 AA approximate tandem repeats of T-T-S-T-T-S-A-P ), compositionally biased region (Thr-rich ), compositionally biased region (Ser-rich ), sequence conflict (In Ref. 2; CAC83674. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Gel-forming glycoprotein of gastric and respiratoy tract epithelia that protects the mucosa from infection and chemical damage by binding to inhaled microrganisms and particles that are subsequently removed by the mucocilary system.; ",{"$nulls":4},"p.Pro2328fs","c.6981_6992del<DELETE_NUC>insC","HIGH","2328/5654",31,{"$nulls":20},"1185390",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr11:1185126:<DELETE_NUC>:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","MUC5AC","chr11:1185126","MUC5AC(P2328fs)",null,null,"region of interest (9 X Cys-rich subdomain repeats ), region of interest (107 X 8 AA approximate tandem repeats of T-T-S-T-T-S-A-P ), compositionally biased region (Thr-rich ), compositionally biased region (Ser-rich ), sequence conflict (In Ref. 2; CAC83674. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Gel-forming glycoprotein of gastric and respiratoy tract epithelia that protects the mucosa from infection and chemical damage by binding to inhaled microrganisms and particles that are subsequently removed by the mucocilary system.; ",{"$nulls":4},"p.Pro2328fs","c.6981_6992del<DELETE_NUC>insC","HIGH","2328/5654",31,{"$nulls":20},"1185390",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr11:1185126:<DELETE_NUC>:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MYBPC2","chr19:50437713","MYBPC2(K189N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Thick filament-associated protein located in the crossbridge region of vertebrate striated muscle a bands. In vitro it binds MHC, F-actin and native thin filaments, and modifies the activity of actin-activated myosin ATPase. It may modulate muscle contraction or may play a more structural role.; ",{"$nulls":4},"p.Lys189Asn","c.567G>C","MODERATE","189/1141",7,{"$nulls":5},"5","158","148","115","113","150","136","0","0","0","0.375",{"$nulls":20},"3.40991","-0.25","2.775","0.798359","-3.9","0.941","0.002","0.639",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","157,0","0","157","0/1","94,54","0.3649","148",null,"chr19:50437713:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3451"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","MYBPC2","chr19:50437713","MYBPC2(K189N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Thick filament-associated protein located in the crossbridge region of vertebrate striated muscle a bands. In vitro it binds MHC, F-actin and native thin filaments, and modifies the activity of actin-activated myosin ATPase. It may modulate muscle contraction or may play a more structural role.; ",{"$nulls":4},"p.Lys189Asn","c.567G>C","MODERATE","189/1141",7,{"$nulls":5},"5","158","224","115","172","150","203","0","0","0","0.3842",{"$nulls":20},"3.40991","-0.25","2.775","0.798359","-3.9","0.941","0.002","0.639",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","157,0","0","157","0/1","133,87","0.3955","220",null,"chr19:50437713:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.407"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","MYLPF","chr16:30375863","MYLPF(S15F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser15Phe","c.44C>T","MODERATE","15/199",1,{"$nulls":5},"5","396","411","255","262","363","367","0","0","0","0.2997",{"$nulls":20},"3.919143","-1.71;-1.77;-1.09;-1.27",".;.;3.725;.","1","-5.25;-5.24;-5.26;-5.36",".;.;0.997;.","0.0",".;.;0.785;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","379,0","0","379","0/1","273,125","0.3141","398",null,"chr16:30375863:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3015"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","MYLPF","chr16:30375863","MYLPF(S15F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser15Phe","c.44C>T","MODERATE","15/199",1,{"$nulls":5},"5","396","486","255","346","363","444","0","0","0","0.3559",{"$nulls":20},"3.919143","-1.71;-1.77;-1.09;-1.27",".;.;3.725;.","1","-5.25;-5.24;-5.26;-5.36",".;.;0.997;.","0.0",".;.;0.785;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","371,0","0","371","0/1","290,177","0.379","467",null,"chr16:30375863:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3642"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","NDN","chr15:23687058","NDN(A54S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Growth suppressor that facilitates the entry of the cell into cell cycle arrest. Functionally similar to the retinoblastoma protein it binds to and represses the activity of cell-cycle- promoting proteins such as SV40 large T antigen, adenovirus E1A, and the transcription factor E2F. Necdin also interacts with p53 and works in an additive manner to inhibit cell growth. Functions also as transcription factor and binds directly to specific guanosine-rich DNA sequences (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala54Ser","c.160G>T","MODERATE","54/321",1,{"$nulls":5},"4","286","209","244","186","212","160","0","0","0","0.2562",{"$nulls":20},"0.643136","4.38;.","0.895","1","-0.36;.","0.041","0.142;.","0.09;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0032897","0/0","277,0","0","277","0/1","163,42","0.2049","205",null,"chr15:23687058:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1989"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","NDN","chr15:23687058","NDN(A54S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Growth suppressor that facilitates the entry of the cell into cell cycle arrest. Functionally similar to the retinoblastoma protein it binds to and represses the activity of cell-cycle- promoting proteins such as SV40 large T antigen, adenovirus E1A, and the transcription factor E2F. Necdin also interacts with p53 and works in an additive manner to inhibit cell growth. Functions also as transcription factor and binds directly to specific guanosine-rich DNA sequences (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala54Ser","c.160G>T","MODERATE","54/321",1,{"$nulls":5},"4","286","237","244","207","212","190","0","0","0","0.3368",{"$nulls":20},"0.643136","4.38;.","0.895","1","-0.36;.","0.041","0.142;.","0.09;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0032897","0/0","276,1","0.0036","277","0/1","157,75","0.3233","232",null,"chr15:23687058:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3285"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","NFKB2","chr10:102400420","NFKB2(E576V)",null,null,"repeat (ANK 3 ), splice variant (In isoform 3. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving NFKB2 is found in a case of B-cell non Hodgkin lymphoma (B-NHL). Translocation t(10;14)(q24;q32) with IGHA1. The resulting oncogene is also called Lyt-10C alpha variant.; DISEASE: Note=A chromosomal aberration involving NFKB2 is found in a cutaneous T-cell leukemia (C-TCL) cell line. This rearrangement produces the p80HT gene which codes for a truncated 80 kDa protein (p80HT).; DISEASE: Note=In B-cell leukemia (B-CLL) cell line, LB40 and EB308, can be found after heterogeneous chromosomal aberrations, such as internal deletions.; DISEASE: Immunodeficiency, common variable, 10 (CVID10) [MIM:615577]: A primary immunodeficiency characterized by childhood-onset of recurrent infections, hypogammaglobulinemia, and decreased numbers of memory and marginal zone B-cells. Some patients may develop autoimmune features and have circulating autoantibodies. An unusual feature is central adrenal insufficiency. {ECO:0000269|PubMed:24140114, ECO:0000269|PubMed:25524009}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF- kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. In a non-canonical activation pathway, the MAP3K14- activated CHUK/IKKA homodimer phosphorylates NFKB2/p100 associated with RelB, inducing its proteolytic processing to NFKB2/p52 and the formation of NF-kappa-B RelB-p52 complexes. The NF-kappa-B heterodimeric RelB-p52 complex is a transcriptional activator. The NF-kappa-B p52-p52 homodimer is a transcriptional repressor. NFKB2 appears to have dual functions such as cytoplasmic retention of attached NF-kappa-B proteins by p100 and generation of p52 by a cotranslational processing. The proteasome-mediated process ensures the production of both p52 and p100 and preserves their independent function. p52 binds to the kappa-B consensus sequence 5'-GGRNNYYCC-3', located in the enhancer region of genes involved in immune response and acute phase reactions. p52 and p100 are respectively the minor and major form; the processing of p100 being relatively poor. Isoform p49 is a subunit of the NF-kappa-B protein complex, which stimulates the HIV enhancer in synergy with p65. In concert with RELB, regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK- ARNTL/BMAL1 heterodimer. {ECO:0000269|PubMed:7925301}.; ","gedi|level2",{"$nulls":3},"p.Glu576Val","c.1727A>T","MODERATE","576/900",16,{"$nulls":5},"5","371","292","285","206","326","268","0","0","0","0.2873",{"$nulls":20},"1.158225","-0.6","1.175","1","-1.4",".;0.001;.","0.248;0.247;0.247","0.359;0.358;0.362",{"$nulls":3},"Unknown",-1,"AD","Immunodeficiency, common variable, 10","Allergy/Immunology/Infectious; Endocrine","COSMIC,kCANCER,kMAPK",null,null,"C3809991","0/0","362,0","0","362","0/1","213,78","0.268","291",null,"chr10:102400420:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2282"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","NFKB2","chr10:102400420","NFKB2(E576V)",null,null,"repeat (ANK 3 ), splice variant (In isoform 3. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving NFKB2 is found in a case of B-cell non Hodgkin lymphoma (B-NHL). Translocation t(10;14)(q24;q32) with IGHA1. The resulting oncogene is also called Lyt-10C alpha variant.; DISEASE: Note=A chromosomal aberration involving NFKB2 is found in a cutaneous T-cell leukemia (C-TCL) cell line. This rearrangement produces the p80HT gene which codes for a truncated 80 kDa protein (p80HT).; DISEASE: Note=In B-cell leukemia (B-CLL) cell line, LB40 and EB308, can be found after heterogeneous chromosomal aberrations, such as internal deletions.; DISEASE: Immunodeficiency, common variable, 10 (CVID10) [MIM:615577]: A primary immunodeficiency characterized by childhood-onset of recurrent infections, hypogammaglobulinemia, and decreased numbers of memory and marginal zone B-cells. Some patients may develop autoimmune features and have circulating autoantibodies. An unusual feature is central adrenal insufficiency. {ECO:0000269|PubMed:24140114, ECO:0000269|PubMed:25524009}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52. The dimers bind at kappa-B sites in the DNA of their target genes and the individual dimers have distinct preferences for different kappa-B sites that they can bind with distinguishable affinity and specificity. Different dimer combinations act as transcriptional activators or repressors, respectively. NF-kappa-B is controlled by various mechanisms of post-translational modification and subcellular compartmentalization as well as by interactions with other cofactors or corepressors. NF-kappa-B complexes are held in the cytoplasm in an inactive state complexed with members of the NF- kappa-B inhibitor (I-kappa-B) family. In a conventional activation pathway, I-kappa-B is phosphorylated by I-kappa-B kinases (IKKs) in response to different activators, subsequently degraded thus liberating the active NF-kappa-B complex which translocates to the nucleus. In a non-canonical activation pathway, the MAP3K14- activated CHUK/IKKA homodimer phosphorylates NFKB2/p100 associated with RelB, inducing its proteolytic processing to NFKB2/p52 and the formation of NF-kappa-B RelB-p52 complexes. The NF-kappa-B heterodimeric RelB-p52 complex is a transcriptional activator. The NF-kappa-B p52-p52 homodimer is a transcriptional repressor. NFKB2 appears to have dual functions such as cytoplasmic retention of attached NF-kappa-B proteins by p100 and generation of p52 by a cotranslational processing. The proteasome-mediated process ensures the production of both p52 and p100 and preserves their independent function. p52 binds to the kappa-B consensus sequence 5'-GGRNNYYCC-3', located in the enhancer region of genes involved in immune response and acute phase reactions. p52 and p100 are respectively the minor and major form; the processing of p100 being relatively poor. Isoform p49 is a subunit of the NF-kappa-B protein complex, which stimulates the HIV enhancer in synergy with p65. In concert with RELB, regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK- ARNTL/BMAL1 heterodimer. {ECO:0000269|PubMed:7925301}.; ","gedi|level2",{"$nulls":3},"p.Glu576Val","c.1727A>T","MODERATE","576/900",16,{"$nulls":5},"5","371","310","285","224","326","273","0","0","0","0.315",{"$nulls":20},"1.158225","-0.6","1.175","1","-1.4",".;0.001;.","0.248;0.247;0.247","0.359;0.358;0.362",{"$nulls":3},"Unknown",-1,"AD","Immunodeficiency, common variable, 10","Allergy/Immunology/Infectious; Endocrine","COSMIC,kCANCER,kMAPK",null,null,"C3809991","0/0","358,0","0","358","0/1","197,100","0.3367","297",null,"chr10:102400420:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3571"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","NKTR","chr3:42637100","NKTR(E466Q)",{"$nulls":3},"compositionally-biased-region:Arg/Ser-rich","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). Component of a putative tumor-recognition complex involved in the function of NK cells (PubMed:8421688). {ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:8421688}.; ",{"$nulls":4},"p.Glu466Gln","c.1396G>C","MODERATE","466/1462",13,{"$nulls":5},"5","168","104","126","81","143","86","0","0","0","0.2907",{"$nulls":20},"3.161544","2.57;.","2.135;.","0.999672","-1.42;.","0.534;.","0.004;.","0.255;0.323",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a membrane-anchored protein with a hydrophobic amino terminal domain and a cyclophilin-like PPIase domain. It is present on the surface of natural killer cells and facilitates their binding to targets. Its expression is regulated by IL2 activation of the cells. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","162,0","0","162","0/1","74,28","0.2745","102",null,"chr3:42637100:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.284"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","NKTR","chr3:42637100","NKTR(E466Q)",{"$nulls":3},"compositionally-biased-region:Arg/Ser-rich","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). Component of a putative tumor-recognition complex involved in the function of NK cells (PubMed:8421688). {ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:8421688}.; ",{"$nulls":4},"p.Glu466Gln","c.1396G>C","MODERATE","466/1462",13,{"$nulls":5},"5","168","146","126","114","143","123","0","0","0","0.3984",{"$nulls":20},"3.161544","2.57;.","2.135;.","0.999672","-1.42;.","0.534;.","0.004;.","0.255;0.323",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a membrane-anchored protein with a hydrophobic amino terminal domain and a cyclophilin-like PPIase domain. It is present on the surface of natural killer cells and facilitates their binding to targets. Its expression is regulated by IL2 activation of the cells. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","166,0","0","166","0/1","92,51","0.3566","143",null,"chr3:42637100:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3246"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","NLGN3","chrX:71167093","NLGN3(S332R)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Asperger syndrome, X-linked, 1 (ASPGX1) [MIM:300494]: A syndrome with features similar to autism. Affected individuals exhibit qualitative impairment in social interaction, as manifest by impairment in the use of non-verbal behaviors such as eye-to- eye gaze, facial expression, body postures, and gestures, failure to develop appropriate peer relationships, and lack of social sharing or reciprocity. Patients also exhibit restricted, repetitive and stereotyped patterns of behavior, interests, and activities, including abnormal preoccupation with certain activities and inflexible adherence to routines or rituals. Asperger syndrome is primarily distinguished from autism by the higher cognitive abilities and a more normal and timely development of language and communicative phrases. {ECO:0000269|PubMed:12669065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Cell surface protein involved in cell-cell-interactions via its interactions with neurexin family members. Plays a role in synapse function and synaptic signal transmission, and may mediate its effects by clustering other synaptic proteins. May promote the initial formation of synapses, but is not essential for this. May also play a role in glia-glia or glia-neuron interactions in the developing peripheral nervous system (By similarity). {ECO:0000250, ECO:0000269|PubMed:15620359}.; ",{"$nulls":4},"p.Ser332Arg","c.996C>A","MODERATE","332/848",7,{"$nulls":5},"4","505","610","412","530","452","519","0","0","0","0.0713",{"$nulls":20},"1.291372","-0.19;.;-0.19;-0.19;-0.19",".;.;.;.;-0.545","0.994486","2.73;.;2.68;2.7;2.66",".;.;.;0.0;0.0","1.0;.;1.0;1.0;1.0","0.267;0.258;.;0.258;0.253",{"$nulls":3},"Unknown",-1,"XL","Asperger syndrome, X-linked 1; Autism, X-linked 1","Neurologic",{"$nulls":3},"C1845540| C1845341","0/0","498,1","0.002","499","0/1","561,41","0.0681","602",null,"chrX:71167093:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0623"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","NOL10","chr2:10667262","NOL10(D183Y)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp183Tyr","c.547G>T","MODERATE","183/688",8,{"$nulls":5},"5","372","335","248","218","345","291","0","0","0","0.1649",{"$nulls":20},"4.5856010000000005","-2.2","2.505;.;2.505;.","1","-4.25;-4.21;-4.25;-4.53","0.993;.;0.835;.","0.007;0.005;0.006;0.002","0.794;0.806;0.794;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","359,0","0","359","0/1","269,55","0.1698","324",null,"chr2:10667262:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1606"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","NOL10","chr2:10667262","NOL10(D183Y)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp183Tyr","c.547G>T","MODERATE","183/688",8,{"$nulls":5},"5","372","526","248","357","344","478","0","0","0","0.1715",{"$nulls":20},"4.5856010000000005","-2.2","2.505;.;2.505;.","1","-4.25;-4.21;-4.25;-4.53","0.993;.;0.835;.","0.007;0.005;0.006;0.002","0.794;0.806;0.794;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","429,92","0.1766","521",null,"chr2:10667262:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1653"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","OR52E6","chr11:5841123","OR52E6(S263P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser263Pro","c.787T>C","MODERATE","263/317",2,{"$nulls":5},"4","296","281","246","233","252","245","0","0","0","0.0694",{"$nulls":20},"2.720152","8.75","4.165;.","1","-4.81","0.998;.","0.0","0.279;0.291",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","298,0","0","298","0/1","261,18","0.0645","279",null,"chr11:5841123:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0601"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","OR5K1","chr3:98470286","OR5K1(S239fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser239fs","c.715dupT","HIGH","239/308",1,{"$nulls":5},"5","540","366","383","251","499","377","0","0","0","0.2042",{"$nulls":5},"(OR5K1|ENSG00000232382|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","469,0","0","469","0/1","261,71","0.2139","332",null,"chr3:98470286:C:CT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2191"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","OR5K1","chr3:98470286","OR5K1(S239fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser239fs","c.715dupT","HIGH","239/308",1,{"$nulls":5},"5","540","434","383","317","499","474","0","0","0","0.2511",{"$nulls":5},"(OR5K1|ENSG00000232382|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","469,0","0","469","0/1","284,116","0.29","400",null,"chr3:98470286:C:CT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2902"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","OTOP2","chr17:74927278","OTOP2(T169I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Proton-selective channel that specifically transports protons into cells. Proton-selective channel activity is probably required in cell types that use changes in intracellular pH for cell signaling or to regulate biochemical or developmental processes. {ECO:0000250|UniProtKB:Q80SX5}.; ",{"$nulls":4},"p.Thr169Ile","c.506C>T","MODERATE","169/562",4,{"$nulls":5},"5","563","629","387","430","516","574","0","0","0","0.1568",{"$nulls":20},"3.543421","1.96","2.955","0.99999","-3.59;.","1.0","0.001;.","0.879;0.88",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","544,0","0","544","0/1","515,100","0.1626","615",null,"chr17:74927278:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1605"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","OTOP2","chr17:74927278","OTOP2(T169I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Proton-selective channel that specifically transports protons into cells. Proton-selective channel activity is probably required in cell types that use changes in intracellular pH for cell signaling or to regulate biochemical or developmental processes. {ECO:0000250|UniProtKB:Q80SX5}.; ",{"$nulls":4},"p.Thr169Ile","c.506C>T","MODERATE","169/562",4,{"$nulls":5},"5","563","692","387","462","517","626","0","0","0","0.1597",{"$nulls":20},"3.543421","1.96","2.955","0.99999","-3.59;.","1.0","0.001;.","0.879;0.88",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","537,0","0","537","0/1","549,116","0.1744","665",null,"chr17:74927278:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PABPC1L","chr20:44933070","PABPC1L(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.1331-2A>T","HIGH",null,9,1,{"$nulls":4},"5","540","742","426","585","402","560","0.0019","0.0019","0","0.1607",{"$nulls":5},"(PABPC1L|ENSG00000101104|1|1.00)",{"$nulls":14},"2.330056",null,null,"0.975831;0.975831;0.975831;0.999338;0.999338;0.975831",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","522,0","0","522","0/1","618,105","0.1452","723",null,"chr20:44933070:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1504"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","PABPC1L","chr20:44933070","PABPC1L(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.1331-2A>T","HIGH",null,9,1,{"$nulls":4},"5","540","848","426","661","400","607","0.0019","0.0019","0","0.1582",{"$nulls":5},"(PABPC1L|ENSG00000101104|1|1.00)",{"$nulls":14},"2.330056",null,null,"0.975831;0.975831;0.975831;0.999338;0.999338;0.975831",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","524,0","0","524","0/1","694,126","0.1537","820",null,"chr20:44933070:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1377"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PCDHB13","chr5:141216020","PCDHB13(R633C)",null,null,"topological domain (Extracellular ), domain (Cadherin 6 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Arg633Cys","c.1897C>T","MODERATE","633/798",1,{"$nulls":5},"4","398","209","313","185","549","70","0","0","0","0.4",{"$nulls":20},"2.692759","0.69","3.03","0.984627","-7.45","1.0",null,"0.34",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","396,0","0","396","0/1","106,101","0.4879","207",null,"chr5:141216020:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4919"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","PCDHB13","chr5:141216020","PCDHB13(R633C)",null,null,"topological domain (Extracellular ), domain (Cadherin 6 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Arg633Cys","c.1897C>T","MODERATE","633/798",1,{"$nulls":5},"4","398","288","313","241","550","111","0","0","0","0.6216",{"$nulls":20},"2.692759","0.69","3.03","0.984627","-7.45","1.0",null,"0.34",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","396,0","0","396","0/1","106,177","0.6254","283",null,"chr5:141216020:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6141"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PCLO","chr7:82915997","PCLO(Q3984fs)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pontocerebellar hypoplasia 3 (PCH3) [MIM:608027]: A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum. Brain MRI shows an abnormally small cerebellum and brainstem, decreased cerebral white matter, and a thin corpus callosum. PCH3 features include seizures, short stature, optic atrophy, progressive microcephaly, severe developmental delay. {ECO:0000269|PubMed:25832664}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May act as a scaffolding protein involved in the organization of synaptic active zones and in synaptic vesicle trafficking. {ECO:0000250|UniProtKB:Q9QYX7}.; ",{"$nulls":4},"p.Gln3984fs","c.11949_11988delCCAACCCCTTATGATAGCACCTGTTTCTACGGATAACACA","HIGH","3983/5142",7,{"$nulls":5},"5","902","647","703","513","930","668","0","0","0","0.1901",{"$nulls":5},"(PCLO|ENSG00000186472|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":6},"C1842687","0/0","1216,0","0","1216","0/1","709,115","0.1396","824",null,"chr7:82915997:ATGTGTTATCCGTAGAAACAGGTGCTATCATAAGGGGTTGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2027"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","PCLO","chr7:82915997","PCLO(Q3984fs)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pontocerebellar hypoplasia 3 (PCH3) [MIM:608027]: A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum. Brain MRI shows an abnormally small cerebellum and brainstem, decreased cerebral white matter, and a thin corpus callosum. PCH3 features include seizures, short stature, optic atrophy, progressive microcephaly, severe developmental delay. {ECO:0000269|PubMed:25832664}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May act as a scaffolding protein involved in the organization of synaptic active zones and in synaptic vesicle trafficking. {ECO:0000250|UniProtKB:Q9QYX7}.; ",{"$nulls":4},"p.Gln3984fs","c.11949_11988delCCAACCCCTTATGATAGCACCTGTTTCTACGGATAACACA","HIGH","3983/5142",7,{"$nulls":5},"4","902","747","703","616","930","791","0","0","0","0.2187",{"$nulls":5},"(PCLO|ENSG00000186472|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":6},"C1842687","0/0","1217,0","0","1217","0/1","790,128","0.1394","918",null,"chr7:82915997:ATGTGTTATCCGTAGAAACAGGTGCTATCATAAGGGGTTGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2321"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PFN2","chr3:149968520","PFN2(D55H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG.; ",{"$nulls":4},"p.Asp55His","c.163G>C","MODERATE","55/188",2,{"$nulls":5},"4","455","535","291","353","403","456","0","0","0","0.0768",{"$nulls":20},"4.218193","-2.15;-2.15;.;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15;-2.15","3.465;3.465;.;.;.;.;.;.;.;.;.;.;.","1","-6.09;-6.09;.;-6.24;-5.89;-5.89;-6.19;-5.89;-5.89;-5.89;-5.89;-5.89;-6.35",".;1.0;.;1.0;1.0;1.0;.;.;.;.;.;.;.","0.001;0.001;.;0.001;0.002;0.002;0.001;0.002;0.002;0.002;0.002;0.002;0.001","0.955;0.966;.;0.958;0.96;0.963;0.956;0.962;0.962;0.962;0.962;0.962;0.933",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a ubiquitous actin monomer-binding protein belonging to the profilin family. It is thought to regulate actin polymerization in response to extracellular signals. There are two alternatively spliced transcript variants encoding different isoforms described for this gene. [provided by RefSeq, Jul 2008].",null,null,"0/0","423,0","0","423","0/1","446,46","0.0935","492",null,"chr3:149968520:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1048"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PLB1","chr2:28600822","PLB1(Q830*)",null,null,"topological domain (Extracellular ), repeat (3 ), region of interest (4 X 308-326 AA approximate repeats ), splice variant (In isoform 5. ), splice variant (In isoform 4. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Membrane-associated phospholipase. Exhibits a calcium- independent broad substrate specificity including phospholipase A2/lysophospholipase activity. Preferential hydrolysis at the sn-2 position of diacylphospholipids and diacyglycerol, whereas it shows no positional specificity toward triacylglycerol. Exhibits also esterase activity toward p-nitrophenyl. May act on the brush border membrane to facilitate the absorption of digested lipids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gln830*","c.2488C>T","HIGH","830/1458",36,{"$nulls":5},"5","184","191","132","140","161","171","0","0","0","0.2573",{"$nulls":5},"(PLB1|ENSG00000163803|1|1.00)","(PLB1|ENSG00000163803|1|1.00)",{"$nulls":13},"8.753025000000001",null,null,"1",{"$nulls":3},"0.863;0.864",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","180,0","0","180","0/1","141,47","0.25","188",null,"chr2:28600822:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2857"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","PLB1","chr2:28600822","PLB1(Q830*)",null,null,"topological domain (Extracellular ), repeat (3 ), region of interest (4 X 308-326 AA approximate repeats ), splice variant (In isoform 5. ), splice variant (In isoform 4. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Membrane-associated phospholipase. Exhibits a calcium- independent broad substrate specificity including phospholipase A2/lysophospholipase activity. Preferential hydrolysis at the sn-2 position of diacylphospholipids and diacyglycerol, whereas it shows no positional specificity toward triacylglycerol. Exhibits also esterase activity toward p-nitrophenyl. May act on the brush border membrane to facilitate the absorption of digested lipids (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gln830*","c.2488C>T","HIGH","830/1458",36,{"$nulls":5},"5","184","263","132","193","156","231","0","0","0","0.3203",{"$nulls":5},"(PLB1|ENSG00000163803|1|1.00)","(PLB1|ENSG00000163803|1|1.00)",{"$nulls":13},"8.753025000000001",null,null,"1",{"$nulls":3},"0.863;0.864",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,0","0","181","0/1","179,80","0.3089","259",null,"chr2:28600822:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3109"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","POLD1","chr19:50415548","POLD1(S918C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Colorectal cancer 10 (CRCS10) [MIM:612591]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24501277}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL) [MIM:615381]: An autosomal dominant systemic disorder characterized by prominent loss of subcutaneous fat, metabolic abnormalities including insulin resistance and diabetes mellitus, sclerodermatous skin, and a facial appearance characterized by mandibular hypoplasia. Sensorineural deafness occurs late in the first or second decades of life. {ECO:0000269|PubMed:23770608}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: As the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), plays a crucial role in high fidelity genome replication, including in lagging strand synthesis, and repair. Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:16510448, PubMed:19074196, PubMed:20334433, PubMed:24035200, PubMed:24022480). Requires the presence of accessory proteins POLD2, POLD3 and POLD4 for full activity. Depending upon the absence (Pol-delta3) or the presence of POLD4 (Pol-delta4), displays differences in catalytic activity. Most notably, expresses higher proofreading activity in the context of Pol-delta3 compared with that of Pol-delta4 (PubMed:19074196, PubMed:20334433). Although both Pol-delta3 and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may be better suited to fulfill this task, exhibiting near-absence of strand displacement activity compared to Pol-delta4 and stalling on encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling process may avoid the formation of a gap, while maintaining a nick that can be readily ligated (PubMed:24035200). Along with DNA polymerase kappa, DNA polymerase delta carries out approximately half of nucleotide excision repair (NER) synthesis following UV irradiation (PubMed:20227374). Under conditions of DNA replication stress, in the presence of POLD3 and POLD4, may catalyze the repair of broken replication forks through break-induced replication (BIR) (PubMed:24310611). Involved in the translesion synthesis (TLS) of templates carrying O6-methylguanine or abasic sites (PubMed:19074196). {ECO:0000269|PubMed:16510448, ECO:0000269|PubMed:19074196, ECO:0000269|PubMed:20227374, ECO:0000269|PubMed:20334433, ECO:0000269|PubMed:24022480, ECO:0000269|PubMed:24035200, ECO:0000269|PubMed:24310611}.; ","level2",{"$nulls":3},"p.Ser918Cys","c.2753C>G","MODERATE","918/1133",20,{"$nulls":5},"5","1051","1042","678","655","933","915","0","0","0","0.3104",{"$nulls":20},"2.675713","2.12;.;2.12;2.12","2.01;.;.;2.01","0.959054","-2.83;.;.;.","0.398;.;.;0.398","0.01;.;.;.","0.185;0.171;0.171;0.186",{"$nulls":3},"Unknown",-1,"AD","Colorectal cancer, susceptibility to, 10","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Endocrine; Musculoskeletal; Oncologic",{"$nulls":3},"C2675481| C3715192","0/0","980,0","0","980","0/1","665,315","0.3214","980",null,"chr19:50415548:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3084"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","POLD1","chr19:50415548","POLD1(S918C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Colorectal cancer 10 (CRCS10) [MIM:612591]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24501277}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL) [MIM:615381]: An autosomal dominant systemic disorder characterized by prominent loss of subcutaneous fat, metabolic abnormalities including insulin resistance and diabetes mellitus, sclerodermatous skin, and a facial appearance characterized by mandibular hypoplasia. Sensorineural deafness occurs late in the first or second decades of life. {ECO:0000269|PubMed:23770608}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: As the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), plays a crucial role in high fidelity genome replication, including in lagging strand synthesis, and repair. Exhibits both DNA polymerase and 3'- to 5'-exonuclease activities (PubMed:16510448, PubMed:19074196, PubMed:20334433, PubMed:24035200, PubMed:24022480). Requires the presence of accessory proteins POLD2, POLD3 and POLD4 for full activity. Depending upon the absence (Pol-delta3) or the presence of POLD4 (Pol-delta4), displays differences in catalytic activity. Most notably, expresses higher proofreading activity in the context of Pol-delta3 compared with that of Pol-delta4 (PubMed:19074196, PubMed:20334433). Although both Pol-delta3 and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may be better suited to fulfill this task, exhibiting near-absence of strand displacement activity compared to Pol-delta4 and stalling on encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling process may avoid the formation of a gap, while maintaining a nick that can be readily ligated (PubMed:24035200). Along with DNA polymerase kappa, DNA polymerase delta carries out approximately half of nucleotide excision repair (NER) synthesis following UV irradiation (PubMed:20227374). Under conditions of DNA replication stress, in the presence of POLD3 and POLD4, may catalyze the repair of broken replication forks through break-induced replication (BIR) (PubMed:24310611). Involved in the translesion synthesis (TLS) of templates carrying O6-methylguanine or abasic sites (PubMed:19074196). {ECO:0000269|PubMed:16510448, ECO:0000269|PubMed:19074196, ECO:0000269|PubMed:20227374, ECO:0000269|PubMed:20334433, ECO:0000269|PubMed:24022480, ECO:0000269|PubMed:24035200, ECO:0000269|PubMed:24310611}.; ","level2",{"$nulls":3},"p.Ser918Cys","c.2753C>G","MODERATE","918/1133",20,{"$nulls":5},"4","1051","1207","678","811","935","1053","0","0","0","0.3656",{"$nulls":20},"2.675713","2.12;.;2.12;2.12","2.01;.;.;2.01","0.959054","-2.83;.;.;.","0.398;.;.;0.398","0.01;.;.;.","0.185;0.171;0.171;0.186",{"$nulls":3},"Unknown",-1,"AD","Colorectal cancer, susceptibility to, 10","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Endocrine; Musculoskeletal; Oncologic",{"$nulls":3},"C2675481| C3715192","0/0","995,0","0","995","0/1","736,425","0.3661","1161",null,"chr19:50415548:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3674"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PPP6R1","chr19:55245631","PPP6R1(T86_Q91del)",null,null,"region of interest (Interaction with PPP6C )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Regulatory subunit of protein phosphatase 6 (PP6). May function as a scaffolding PP6 subunit. Involved in the PP6- mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF-alpha. {ECO:0000269|PubMed:16769727}.; ",{"$nulls":4},"p.Thr86_Gln91del","c.257_274delCCTCAGATGTGCCCCAGA","MODERATE","86/881",3,{"$nulls":5},"4","477","516","350","389","363","373","0.0022","0.0022","0","0.1233",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","465,0","0","465","0/1","438,65","0.1292","503",null,"chr19:55245631:ATCTGGGGCACATCTGAGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1157"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","PTPRN","chr2:219296755","PTPRN(S768R)",null,null,"topological domain (Cytoplasmic ), domain (Tyrosine-protein phosphatase ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Autoantigen in insulin-dependent diabetes mellitus (IDDM). {ECO:0000269|PubMed:8144912, ECO:0000269|PubMed:8641276}.; ","FUNCTION: Plays a role in vesicle-mediated secretory processes (PubMed:24843546). Required for normal accumulation of secretory vesicles in hippocampus, pituitary and pancreatic islets (By similarity). Required for the accumulation of normal levels of insulin-containing vesicles and preventing their degradation (PubMed:24843546). Plays a role in insulin secretion in response to glucose stimuli (PubMed:24843546). Required for normal accumulation of the neurotransmitters norepinephrine, dopamine and serotonin in the brain (By similarity). In females, but not in males, required for normal accumulation and secretion of pituitary hormones, such as luteinizing hormone (LH) and follicle- stimulating hormone (FSH) (By similarity). Required to maintain normal levels of renin expression and renin release (By similarity). Seems to lack intrinsic enzyme activity (By similarity). May regulate catalytic active protein-tyrosine phosphatases such as PTPRA through dimerization (By similarity). {ECO:0000250|UniProtKB:Q60673, ECO:0000269|PubMed:24843546}.; FUNCTION: ICA512-cleaved cytosolic fragment: ICA512-CCF translocated to the nucleus promotes expression of insulin and other granule-related genes; the function implicates binding to and regulating activity of STAT5B probably by preventing its dephosphorylation and potentially by inducing its sumoylation by recruiting PIAS4 (PubMed:15596545, PubMed:16622421, PubMed:18178618). Enhances pancreatic beta-cell proliferation by converging with signaling by STAT5B and STAT3 (PubMed:15596545, PubMed:16622421, PubMed:18178618). ICA512-CCF located in the cytoplasm regulates dynamics and exocytosis of insulin secretory granules (SGs) by dimerizing with ICA512-TMF and displacing SNTB2 thus enhancing SGs mobility and exocytosis (PubMed:18824546, PubMed:20886068). {ECO:0000269|PubMed:15596545, ECO:0000269|PubMed:16622421, ECO:0000269|PubMed:18178618, ECO:0000269|PubMed:18824546, ECO:0000269|PubMed:20886068}.; ",{"$nulls":4},"p.Ser768Arg","c.2304C>A","MODERATE","768/979",16,{"$nulls":5},"5","372","310","272","234","315","243","0","0","0","0.2016",{"$nulls":20},"3.769492","2.1;2.1;.",".;4.12;.","0.999999;1;0.999999;0.999998","-4.99;-4.99;.",".;1.0;.","0.0;0.0;.","0.978;0.987;0.988",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","355,0","0","355","0/1","240,51","0.1753","291",null,"chr2:219296755:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1624"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","PTPRN","chr2:219296755","PTPRN(S768R)",null,null,"topological domain (Cytoplasmic ), domain (Tyrosine-protein phosphatase ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Autoantigen in insulin-dependent diabetes mellitus (IDDM). {ECO:0000269|PubMed:8144912, ECO:0000269|PubMed:8641276}.; ","FUNCTION: Plays a role in vesicle-mediated secretory processes (PubMed:24843546). Required for normal accumulation of secretory vesicles in hippocampus, pituitary and pancreatic islets (By similarity). Required for the accumulation of normal levels of insulin-containing vesicles and preventing their degradation (PubMed:24843546). Plays a role in insulin secretion in response to glucose stimuli (PubMed:24843546). Required for normal accumulation of the neurotransmitters norepinephrine, dopamine and serotonin in the brain (By similarity). In females, but not in males, required for normal accumulation and secretion of pituitary hormones, such as luteinizing hormone (LH) and follicle- stimulating hormone (FSH) (By similarity). Required to maintain normal levels of renin expression and renin release (By similarity). Seems to lack intrinsic enzyme activity (By similarity). May regulate catalytic active protein-tyrosine phosphatases such as PTPRA through dimerization (By similarity). {ECO:0000250|UniProtKB:Q60673, ECO:0000269|PubMed:24843546}.; FUNCTION: ICA512-cleaved cytosolic fragment: ICA512-CCF translocated to the nucleus promotes expression of insulin and other granule-related genes; the function implicates binding to and regulating activity of STAT5B probably by preventing its dephosphorylation and potentially by inducing its sumoylation by recruiting PIAS4 (PubMed:15596545, PubMed:16622421, PubMed:18178618). Enhances pancreatic beta-cell proliferation by converging with signaling by STAT5B and STAT3 (PubMed:15596545, PubMed:16622421, PubMed:18178618). ICA512-CCF located in the cytoplasm regulates dynamics and exocytosis of insulin secretory granules (SGs) by dimerizing with ICA512-TMF and displacing SNTB2 thus enhancing SGs mobility and exocytosis (PubMed:18824546, PubMed:20886068). {ECO:0000269|PubMed:15596545, ECO:0000269|PubMed:16622421, ECO:0000269|PubMed:18178618, ECO:0000269|PubMed:18824546, ECO:0000269|PubMed:20886068}.; ",{"$nulls":4},"p.Ser768Arg","c.2304C>A","MODERATE","768/979",16,{"$nulls":5},"5","372","363","272","277","312","312","0","0","0","0.234",{"$nulls":20},"3.769492","2.1;2.1;.",".;4.12;.","0.999999;1;0.999999;0.999998","-4.99;-4.99;.",".;1.0;.","0.0;0.0;.","0.978;0.987;0.988",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","356,0","0","356","0/1","280,78","0.2179","358",null,"chr2:219296755:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.213"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","RFX2","chr19:6013021","RFX2(M288I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that acts as a key regulator of spermatogenesis. Acts by regulating expression of genes required for the haploid phase during spermiogenesis, such as genes required for cilium assembly and function (By similarity). Recognizes and binds the X-box, a regulatory motif with DNA sequence 5'-GTNRCC(0-3N)RGYAAC-3' present on promoters (PubMed:10330134). Probably activates transcription of the testis- specific histone gene HIST1H1T (By similarity). {ECO:0000250|UniProtKB:P48379, ECO:0000269|PubMed:10330134}.; ",{"$nulls":4},"p.Met288Ile","c.864G>T","MODERATE","288/723",8,{"$nulls":5},"5","332","251","243","190","273","208","0","0","0","0.3269",{"$nulls":20},"2.508457","-0.11;-0.11;-0.07;-1.64","2.36;2.36;.;.","1","-1.86;.;.;.","0.057;0.057;0.094;.","0.125;.;.;.","0.514;0.514;0.508;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","319,0","0","319","0/1","165,77","0.3182","242",null,"chr19:6013021:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3211"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","RFX2","chr19:6013021","RFX2(M288I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that acts as a key regulator of spermatogenesis. Acts by regulating expression of genes required for the haploid phase during spermiogenesis, such as genes required for cilium assembly and function (By similarity). Recognizes and binds the X-box, a regulatory motif with DNA sequence 5'-GTNRCC(0-3N)RGYAAC-3' present on promoters (PubMed:10330134). Probably activates transcription of the testis- specific histone gene HIST1H1T (By similarity). {ECO:0000250|UniProtKB:P48379, ECO:0000269|PubMed:10330134}.; ",{"$nulls":4},"p.Met288Ile","c.864G>T","MODERATE","288/723",8,{"$nulls":5},"5","332","307","243","221","271","245","0","0","0","0.3102",{"$nulls":20},"2.508457","-0.11;-0.11;-0.07;-1.64","2.36;2.36;.;.","1","-1.86;.;.;.","0.057;0.057;0.094;.","0.125;.;.;.","0.514;0.514;0.508;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","320,0","0","320","0/1","206,93","0.311","299",null,"chr19:6013021:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3077"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","RNF123","chr3:49699055","RNF123(S240fs)",null,null,"domain (B30.2/SPRY )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase. Required for poly-ubiquitination and proteasome-mediated degradation of CDKN1B during G1 phase of the cell cycle. {ECO:0000269|PubMed:15531880, ECO:0000269|PubMed:16227581}.; ",{"$nulls":4},"p.Ser240fs","c.719_720delCT","HIGH","240/1314",10,{"$nulls":5},"4","389","380","250","236","330","385","0","0","0","0.5273",{"$nulls":5},"(RNF123|ENSG00000164068|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","326,0","0","326","0/1","118,217","0.6478","335",null,"chr3:49699055:CCT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5508"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","RNF123","chr3:49699055","RNF123(S240fs)",null,null,"domain (B30.2/SPRY )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase. Required for poly-ubiquitination and proteasome-mediated degradation of CDKN1B during G1 phase of the cell cycle. {ECO:0000269|PubMed:15531880, ECO:0000269|PubMed:16227581}.; ",{"$nulls":4},"p.Ser240fs","c.719_720delCT","HIGH","240/1314",10,{"$nulls":5},"4","389","472","250","298","331","480","0","0","0","0.5708",{"$nulls":5},"(RNF123|ENSG00000164068|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","328,0","0","328","0/1","109,311","0.7405","420",null,"chr3:49699055:CCT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7081"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","RNF32","chr7:156654624","RNF32(D108G)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in sperm formation. {ECO:0000269|PubMed:11890671}.; ",{"$nulls":4},"p.Asp108Gly","c.323A>G","MODERATE","108/362",4,{"$nulls":5},"4","494","815","360","604","413","683","0","0","0","0.0688",{"$nulls":20},"1.532174","-2.99",".;2.24;2.24;2.24;.;2.24;2.24","1","-3.12;-3.51;-3.51;-3.51;-3.11;-3.51;-3.12",".;0.204;0.204;0.204;0.035;0.204;0.082","0.087;0.107;0.107;0.107;0.085;0.107;0.101",".;0.164;0.159;0.165;0.152;0.165;0.138",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","486,0","0","486","0/1","746,51","0.064","797",null,"chr7:156654624:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0596"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","SERPINE2","chr2:223998265","SERPINE2(A125S)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine protease inhibitor with activity toward thrombin, trypsin, and urokinase. Promotes neurite extension by inhibiting thrombin. Binds heparin.; ",{"$nulls":4},"p.Ala125Ser","c.373G>T","MODERATE","125/409",3,{"$nulls":5},"4","1060","618","732","439","955","545","0","0","0","0.3596",{"$nulls":20},"3.598424","-1.82","1.38;1.38;1.38;.;.","1","-0.88;-0.88;-0.88;-0.88;-0.79",".;0.994;.;.;.","0.007;0.101;0.007;0.17;0.008","0.438;0.439;0.438;0.433;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1008,0","0","1008","0/1","369,223","0.3767","592",null,"chr2:223998265:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3622"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","SERPINE2","chr2:223998265","SERPINE2(A125S)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine protease inhibitor with activity toward thrombin, trypsin, and urokinase. Promotes neurite extension by inhibiting thrombin. Binds heparin.; ",{"$nulls":4},"p.Ala125Ser","c.373G>T","MODERATE","125/409",3,{"$nulls":5},"4","1060","797","732","549","957","722","0","0","0","0.3712",{"$nulls":20},"3.598424","-1.82","1.38;1.38;1.38;.;.","1","-0.88;-0.88;-0.88;-0.88;-0.79",".;0.994;.;.;.","0.007;0.101;0.007;0.17;0.008","0.438;0.439;0.438;0.433;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1008,0","0","1008","0/1","478,297","0.3832","775",null,"chr2:223998265:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3916"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","SLC22A17","chr14:23352363","SLC22A17(G62V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell surface receptor for LCN2 (24p3) that plays a key role in iron homeostasis and transport. Able to bind iron-bound LCN2 (holo-24p3), followed by internalization of holo-24p3 and release of iron, thereby increasing intracellular iron concentration and leading to inhibition of apoptosis. Also binds iron-free LCN2 (apo-24p3), followed by internalization of apo-24p3 and its association with an intracellular siderophore, leading to iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration and resulting in apoptosis (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly62Val","c.185G>T","MODERATE","62/631",2,{"$nulls":5},"3","14","12",{"$nulls":4},"0","0",{"$nulls":22},"2.148722",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","15,0","0","15","0/1","8,3","0.2727","11",null,"chr14:23352363:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","SLC2A6","chr9:133479035","SLC2A6(E9K)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs374512440",1.1876484560570071E-4,null,"FUNCTION: Facilitative glucose transporter; binds cytochalasin B with low affinity.; ",{"$nulls":4},"p.Glu9Lys","c.25G>A","MODERATE","9/507",1,1,{"$nulls":4},"5","206","139","130","87","186","121","0","0","0","0.2562",{"$nulls":20},"2.494497","-1.52;-1.58;-2.76","1.905;1.905;.","0.967984","-0.62;-0.62;-0.72","0.017;0.001;0.026","0.024;0.023;0.035","0.337;0.355;.",{"$nulls":3},"ESP6500_EA_AF",1.1876484560570071E-4,{"$nulls":7},"0/0","195,0","0","195","0/1","98,34","0.2576","132",null,"chr9:133479035:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2874"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","SLC2A6","chr9:133479035","SLC2A6(E9K)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs374512440",1.1876484560570071E-4,null,"FUNCTION: Facilitative glucose transporter; binds cytochalasin B with low affinity.; ",{"$nulls":4},"p.Glu9Lys","c.25G>A","MODERATE","9/507",1,1,{"$nulls":4},"5","206","180","130","124","188","164","0","0","0","0.1707",{"$nulls":20},"2.494497","-1.52;-1.58;-2.76","1.905;1.905;.","0.967984","-0.62;-0.62;-0.72","0.017;0.001;0.026","0.024;0.023;0.035","0.337;0.355;.",{"$nulls":3},"ESP6500_EA_AF",1.1876484560570071E-4,{"$nulls":7},"0/0","197,0","0","197","0/1","139,35","0.2011","174",null,"chr9:133479035:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2016"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","SLC7A4","chr22:21029781","SLC7A4(S518I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the transport of the cationic amino acids (arginine, lysine and ornithine).; ",{"$nulls":4},"p.Ser518Ile","c.1553G>T","MODERATE","518/635",3,{"$nulls":5},"5","412","252","315","186","362","218","0","0","0","0.5642",{"$nulls":20},"0.392391","-1.93","1.7","1","-0.62","0.007","0.432","0.313;0.311",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","392,0","0","392","0/1","111,134","0.5469","245",null,"chr22:21029781:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5538"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","SLC7A4","chr22:21029781","SLC7A4(S518I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the transport of the cationic amino acids (arginine, lysine and ornithine).; ",{"$nulls":4},"p.Ser518Ile","c.1553G>T","MODERATE","518/635",3,{"$nulls":5},"5","412","305","315","240","365","271","0","0","0","0.6568",{"$nulls":20},"0.392391","-1.93","1.7","1","-0.62","0.007","0.432","0.313;0.311",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","406,0","0","406","0/1","106,204","0.6581","310",null,"chr22:21029781:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6708"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","SPTLC2","chr14:77570458","SPTLC2(G228R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate. {ECO:0000269|PubMed:19416851, ECO:0000269|PubMed:20920666}.; ","mitocarta",{"$nulls":3},"p.Gly228Arg","c.682G>A","MODERATE","228/562",5,1,{"$nulls":4},"5","436","339","274","226","372","291","0","0","0","0.1649",{"$nulls":20},"3.456365","-4.22","2.11","1","-6.21","0.732","0.021","0.771",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011].  ",null,"C3150896","0/0","421,0","0","421","0/1","277,55","0.1657","332",null,"chr14:77570458:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1726"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","SPTLC2","chr14:77570458","SPTLC2(G228R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate. {ECO:0000269|PubMed:19416851, ECO:0000269|PubMed:20920666}.; ","mitocarta",{"$nulls":3},"p.Gly228Arg","c.682G>A","MODERATE","228/562",5,1,{"$nulls":4},"5","436","438","274","291","370","369","0","0","0","0.206",{"$nulls":20},"3.456365","-4.22","2.11","1","-6.21","0.732","0.021","0.771",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a long chain base subunit of serine palmitoyltransferase. Serine palmitoyltransferase, which consists of two different subunits, is the key enzyme in sphingolipid biosynthesis. It catalyzes the pyridoxal-5-prime-phosphate-dependent condensation of L-serine and palmitoyl-CoA to 3-oxosphinganine. Mutations in this gene were identified in patients with hereditary sensory neuropathy type I. [provided by RefSeq, Mar 2011].  ",null,"C3150896","0/0","411,0","0","411","0/1","334,98","0.2269","432",null,"chr14:77570458:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2131"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","SRGAP3","chr3:9013837","SRGAP3(E607Q)",null,null,"domain (Rho-GAP ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving SRGAP3 is found in a patient with severe idiopathic mental retardation (PubMed:12195014). Translocation t(X;3)(p11.2;p25) (PubMed:12195014). {ECO:0000269|PubMed:12195014}.; ","FUNCTION: GTPase-activating protein for RAC1 and perhaps Cdc42, but not for RhoA small GTPase. May attenuate RAC1 signaling in neurons. {ECO:0000269|PubMed:12195014, ECO:0000269|PubMed:12447388}.; ","level2",{"$nulls":3},"p.Glu607Gln","c.1819G>C","MODERATE","607/1099",16,{"$nulls":5},"4","783","1192","500","824","722","1149","0","0","0","0.3951",{"$nulls":20},"3.206263","0.85;2.14","1.945;.","1","-2.47","0.024;0.016","0.004;0.005","0.489;0.474",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","734,0","0","734","0/1","707,401","0.3619","1108",null,"chr3:9013837:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4005"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","SRGAP3","chr3:9013837","SRGAP3(E607Q)",null,null,"domain (Rho-GAP ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving SRGAP3 is found in a patient with severe idiopathic mental retardation (PubMed:12195014). Translocation t(X;3)(p11.2;p25) (PubMed:12195014). {ECO:0000269|PubMed:12195014}.; ","FUNCTION: GTPase-activating protein for RAC1 and perhaps Cdc42, but not for RhoA small GTPase. May attenuate RAC1 signaling in neurons. {ECO:0000269|PubMed:12195014, ECO:0000269|PubMed:12447388}.; ","level2",{"$nulls":3},"p.Glu607Gln","c.1819G>C","MODERATE","607/1099",16,{"$nulls":5},"4","783","1836","500","1234","713","1721","0","0","0","0.4091",{"$nulls":20},"3.206263","0.85;2.14","1.945;.","1","-2.47","0.024;0.016","0.004;0.005","0.489;0.474",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","727,0","0","727","0/1","1077,634","0.3705","1711",null,"chr3:9013837:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4003"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","TAL1","chr1:47225620","TAL1(T90N)",null,null,"compositionally biased region (Pro-rich ), splice variant (In isoform PP22-TAL1. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving TAL1 may be a cause of some T-cell acute lymphoblastic leukemias (T-ALL). Translocation t(1;14)(p32;q11) with T-cell receptor alpha chain (TCRA) genes. {ECO:0000269|PubMed:2303035}.; ","FUNCTION: Implicated in the genesis of hemopoietic malignancies. It may play an important role in hemopoietic differentiation. Serves as a positive regulator of erythroid differentiation (By similarity). {ECO:0000250, ECO:0000269|PubMed:1396592}.; ","gedi|level2",{"$nulls":3},"p.Thr90Asn","c.269C>A","MODERATE","90/331",2,{"$nulls":5},"5","180","144","123","102","152","120","0","0","0","0.1167",{"$nulls":20},"2.412611","-4.51","1.905","0.895803","-2.15","0.868","0.002","0.178;0.18",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC,vRB,vRB",null,null,"C0023449","0/0","178,0","0","178","0/1","121,16","0.1168","137",null,"chr1:47225620:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1078"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","TAL1","chr1:47225620","TAL1(T90N)",null,null,"compositionally biased region (Pro-rich ), splice variant (In isoform PP22-TAL1. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving TAL1 may be a cause of some T-cell acute lymphoblastic leukemias (T-ALL). Translocation t(1;14)(p32;q11) with T-cell receptor alpha chain (TCRA) genes. {ECO:0000269|PubMed:2303035}.; ","FUNCTION: Implicated in the genesis of hemopoietic malignancies. It may play an important role in hemopoietic differentiation. Serves as a positive regulator of erythroid differentiation (By similarity). {ECO:0000250, ECO:0000269|PubMed:1396592}.; ","gedi|level2",{"$nulls":3},"p.Thr90Asn","c.269C>A","MODERATE","90/331",2,{"$nulls":5},"5","180","242","123","164","152","208","0","0","0","0.1635",{"$nulls":20},"2.412611","-4.51","1.905","0.895803","-2.15","0.868","0.002","0.178;0.18",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC,vRB,vRB",null,null,"C0023449","0/0","178,0","0","178","0/1","197,40","0.1688","237",null,"chr1:47225620:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1768"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","TOP3A","chr17:18285254","TOP3A(E589Q)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Has DNA decatenation activity. {ECO:0000269|PubMed:20445207, ECO:0000269|PubMed:8622991}.; ","level2",{"$nulls":4},"c.1765G>C","HIGH",null,15,{"$nulls":5},"5","554","351","436","280","472","306","0","0","0","0.5948",{"$nulls":20},"3.744592","3.03;1.07;1.07","4.475;4.475;.","1","-0.7;-2.91;.","0.946;0.946;.","0.401;0.003;.","0.937;0.937;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kHOMOLOGOUS_RECOMBINATION","This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which allows the strands to pass through one another, thus reducing the number of supercoils and altering the topology of DNA. This enzyme forms a complex with BLM which functions in the regulation of recombination in somatic cells. [provided by RefSeq, Jul 2008].  ",null,"C4748184| C4748176","0/0","549,0","0","549","0/1","141,207","0.5948","348",null,"chr17:18285254:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6107"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","TOP3A","chr17:18285254","TOP3A(E589Q)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Has DNA decatenation activity. {ECO:0000269|PubMed:20445207, ECO:0000269|PubMed:8622991}.; ","level2",{"$nulls":4},"c.1765G>C","HIGH",null,15,{"$nulls":5},"5","554","378","436","303","473","308","0","0","0","0.6364",{"$nulls":20},"3.744592","3.03;1.07;1.07","4.475;4.475;.","1","-0.7;-2.91;.","0.946;0.946;.","0.401;0.003;.","0.937;0.937;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kHOMOLOGOUS_RECOMBINATION","This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which allows the strands to pass through one another, thus reducing the number of supercoils and altering the topology of DNA. This enzyme forms a complex with BLM which functions in the regulation of recombination in somatic cells. [provided by RefSeq, Jul 2008].  ",null,"C4748184| C4748176","0/0","547,0","0","547","0/1","141,237","0.627","378",null,"chr17:18285254:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6337"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","TP53","chr17:7675084","TP53(C137W)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In sporadic cancers; somatic mutation. TP53(L137M)), sequence variant (In sporadic cancers; somatic mutation. TP53(L137P)), sequence variant (In sporadic cancers; somatic mutation. TP53(L137Q)), sequence variant (In sporadic cancers; somatic mutation. TP53(L137V))",{"$nulls":3},255,"PASS","Missense","rs1057519980",-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Cys137Trp","c.411C>G","MODERATE","137/410",5,31,{"$nulls":4},"5","865","584","618","438","739","521","0","0","0","0.5221",{"$nulls":20},"2.64777","-10.62;-10.62;.;.;.;.;.;.;.;-10.62;.;.;-10.62;-10.62;.;.;-10.62;.;.;-10.62;-10.62",".;.;.;.;.;.;.;.;.;3.335;.;3.335;3.335;3.335;.;.;3.335;.;.;.;.","1","-10.62;-10.58;.;.;.;.;.;.;.;-10.71;.;.;-10.58;-10.58;.;.;-10.71;.;.;-10.11;-10.53","1.0;.;.;.;.;.;.;.;.;1.0;.;1.0;1.0;1.0;.;.;1.0;.;.;.;1.0","0.004;0.004;.;.;.;.;.;.;.;0.004;.;.;0.004;0.004;.;.;0.004;.;.;0.004;0.004","0.956;0.948;0.934;0.951;0.95;0.924;0.951;0.933;0.945;0.945;0.945;0.947;0.945;0.947;0.949;0.92;0.945;0.945;0.939;.;.",{"$nulls":3},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","826,0","0","826","0/1","261,309","0.5421","570",null,"chr17:7675084:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5297"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","TP53","chr17:7675084","TP53(C137W)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In sporadic cancers; somatic mutation. TP53(L137M)), sequence variant (In sporadic cancers; somatic mutation. TP53(L137P)), sequence variant (In sporadic cancers; somatic mutation. TP53(L137Q)), sequence variant (In sporadic cancers; somatic mutation. TP53(L137V))",{"$nulls":3},255,"PASS","Missense","rs1057519980",-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Cys137Trp","c.411C>G","MODERATE","137/410",5,31,{"$nulls":4},"5","865","743","618","532","737","656","0","0","0","0.6296",{"$nulls":20},"2.64777","-10.62;-10.62;.;.;.;.;.;.;.;-10.62;.;.;-10.62;-10.62;.;.;-10.62;.;.;-10.62;-10.62",".;.;.;.;.;.;.;.;.;3.335;.;3.335;3.335;3.335;.;.;3.335;.;.;.;.","1","-10.62;-10.58;.;.;.;.;.;.;.;-10.71;.;.;-10.58;-10.58;.;.;-10.71;.;.;-10.11;-10.53","1.0;.;.;.;.;.;.;.;.;1.0;.;1.0;1.0;1.0;.;.;1.0;.;.;.;1.0","0.004;0.004;.;.;.;.;.;.;.;0.004;.;.;0.004;0.004;.;.;0.004;.;.;0.004;0.004","0.956;0.948;0.934;0.951;0.95;0.924;0.951;0.933;0.945;0.945;0.945;0.947;0.945;0.947;0.949;0.92;0.945;0.945;0.939;.;.",{"$nulls":3},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","821,0","0","821","0/1","263,451","0.6317","714",null,"chr17:7675084:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6241"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","UHRF1BP1L","chr12:100058515","UHRF1BP1L(R921I)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg921Ile","c.2762G>T","MODERATE","921/1464",14,{"$nulls":5},"5","237","117","182","88","212","104","0.0042","0.0042","0","0.2404",{"$nulls":20},"1.682412","2.88","1.7;.","0.999915","-0.87;-0.85","0.394;.","0.129;0.134","0.361;0.333",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","237,1","0.0042","238","0/1","88,27","0.2348","115",null,"chr12:100058515:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2159"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","UHRF1BP1L","chr12:100058515","UHRF1BP1L(R921I)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg921Ile","c.2762G>T","MODERATE","921/1464",14,{"$nulls":5},"5","237","185","182","140","212","167","0.0042","0.0042","0","0.3114",{"$nulls":20},"1.682412","2.88","1.7;.","0.999915","-0.87;-0.85","0.394;.","0.129;0.134","0.361;0.333",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","237,1","0.0042","238","0/1","127,58","0.3135","185",null,"chr12:100058515:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3071"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","USP42","chr7:6149641","USP42(S482*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Deubiquitinating enzyme which may play an important role during spermatogenesis. {ECO:0000250}.; ",{"$nulls":4},"p.Ser482*","c.1445_1446delCGinsAA","HIGH","482/1316",13,{"$nulls":5},"5","321","223","243","170","291","198","0","0","0","0.1869",{"$nulls":5},"(USP42|ENSG00000106346|1|1.00)","(USP42|ENSG00000106346|1|1.00)",{"$nulls":24},"Unknown",-1,{"$nulls":7},"0/0","312,0","0","312","0/1","180,40","0.1818","220",null,"chr7:6149641:CG:AA",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","USP42","chr7:6149641","USP42(S482*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Deubiquitinating enzyme which may play an important role during spermatogenesis. {ECO:0000250}.; ",{"$nulls":4},"p.Ser482*","c.1445_1446delCGinsAA","HIGH","482/1316",13,{"$nulls":5},"5","321","330","243","257","292","302","0","0","0","0.245",{"$nulls":5},"(USP42|ENSG00000106346|1|1.00)","(USP42|ENSG00000106346|1|1.00)",{"$nulls":24},"Unknown",-1,{"$nulls":7},"0/0","312,0","0","312","0/1","250,78","0.2378","328",null,"chr7:6149641:CG:AA",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2296"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","VAV3","chr1:107770695","VAV3(L197V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Exchange factor for GTP-binding proteins RhoA, RhoG and, to a lesser extent, Rac1. Binds physically to the nucleotide-free states of those GTPases. Plays an important role in angiogenesis. Its recruitment by phosphorylated EPHA2 is critical for EFNA1- induced RAC1 GTPase activation and vascular endothelial cell migration and assembly (By similarity). May be important for integrin-mediated signaling, at least in some cell types. In osteoclasts, along with SYK tyrosine kinase, required for signaling through integrin alpha-v/beta-1 (ITAGV-ITGB1), a crucial event for osteoclast proper cytoskeleton organization and function. This signaling pathway involves RAC1, but not RHO, activation. Necessary for proper wound healing. In the course of wound healing, required for the phagocytotic cup formation preceding macrophage phagocytosis of apoptotic neutrophils. Responsible for integrin beta-2 (ITGB2)-mediated macrophage adhesion and, to a lesser extent, contributes to beta-3 (ITGB3)- mediated adhesion. Does not affect integrin beta-1 (ITGB1)- mediated adhesion (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu197Val","c.589C>G","MODERATE","197/875",6,{"$nulls":5},"5","64","45","39","28","58","45","0","0","0","0.0889",{"$nulls":20},"2.9805099999999998","-0.02","2.115","0.999713;0.999713;0.999524","-2.3","0.999;.","0.004","0.667;0.646",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","63,0","0","63","0/1","42,4","0.087","46",null,"chr1:107770695:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1071"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","WWC2","chr4:183284317","WWC2(P1016L)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense","rs745915925",1.211E-4,{"$nulls":6},"p.Pro1016Leu","c.3047C>T","MODERATE","1016/1216",19,{"$nulls":5},"3","462","489","306","334",null,null,"0","0",{"$nulls":22},"2.866813","0.44","2.31;.;.;.;.","1","-7.03;-6.76;-7.03;-8.0;-8.32","1.0;0.999;1.0;.;1.0","0.001;0.001;0.001;0.001;0.002","0.791;0.741;0.543;0.746;0.776",{"$nulls":3},"ExAC_SAS_AF",1.211E-4,{"$nulls":7},"0/0","432,0","0","432","0/1","403,52","0.1143","455",null,"chr4:183284317:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1198"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","WWC2","chr4:183284317","WWC2(P1016L)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense","rs745915925",1.211E-4,{"$nulls":6},"p.Pro1016Leu","c.3047C>T","MODERATE","1016/1216",19,{"$nulls":5},"4","462","644","306","405","432","580","0","0","0","0.1879",{"$nulls":20},"2.866813","0.44","2.31;.;.;.;.","1","-7.03;-6.76;-7.03;-8.0;-8.32","1.0;0.999;1.0;.;1.0","0.001;0.001;0.001;0.001;0.002","0.791;0.741;0.543;0.746;0.776",{"$nulls":3},"ExAC_SAS_AF",1.211E-4,{"$nulls":7},"0/0","439,0","0","439","0/1","497,119","0.1932","616",null,"chr4:183284317:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ZNF146","chr19:36237182","ZNF146(A248P)",null,null,"zinc finger region (C2H2-type 9 ), region of interest (Interaction with TERF2IP )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala248Pro","c.742G>C","MODERATE","248/292",4,{"$nulls":5},"5","378","337","273","242","312","266","0","0","0","0.3684",{"$nulls":20},"3.455716","2.51","1.24","1;0.826782;0.826782","-4.31","1.0","0.001","0.318",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","376,0","0","376","0/1","203,125","0.3811","328",null,"chr19:36237182:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3719"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ZNF146","chr19:36237182","ZNF146(A248P)",null,null,"zinc finger region (C2H2-type 9 ), region of interest (Interaction with TERF2IP )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala248Pro","c.742G>C","MODERATE","248/292",4,{"$nulls":5},"5","378","399","273","298","309","303","0","0","0","0.3663",{"$nulls":20},"3.455716","2.51","1.24","1;0.826782;0.826782","-4.31","1.0","0.001","0.318",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","378,0","0","378","0/1","242,149","0.3811","391",null,"chr19:36237182:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3658"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ZNF200","chr16:3224239","ZNF200(D281N)",null,null,"zinc finger region (C2H2-type 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Could have a role in spermatogenesis.; ",{"$nulls":4},"p.Asp281Asn","c.841G>A","MODERATE","281/395",5,{"$nulls":5},"5","641","471","470","360","556","367","0","0","0","0.1172",{"$nulls":20},"1.8183449999999999","2.29",".;-0.05;.;-0.05;.;.","0.999616","-1.32;.;-1.01;-0.92;.;.","0.981;0.006;.;0.006;.;.","0.017;.;0.009;0.014;.;.","0.125;0.156;0.155;0.158;0.184;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","625,0","0","625","0/1","400,56","0.1228","456",null,"chr16:3224239:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1194"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ZNF200","chr16:3224239","ZNF200(D281N)",null,null,"zinc finger region (C2H2-type 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Could have a role in spermatogenesis.; ",{"$nulls":4},"p.Asp281Asn","c.841G>A","MODERATE","281/395",5,{"$nulls":5},"5","641","683","470","509","558","594","0","0","0","0.1532",{"$nulls":20},"1.8183449999999999","2.29",".;-0.05;.;-0.05;.;.","0.999616","-1.32;.;-1.01;-0.92;.;.","0.981;0.006;.;0.006;.;.","0.017;.;0.009;0.014;.;.","0.125;0.156;0.155;0.158;0.184;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","626,0","0","626","0/1","554,103","0.1568","657",null,"chr16:3224239:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1532"]
["04HS","T11","JLPIKTOR_JLPIKTOR_17113004HS","ZZEF1","chr17:4052023","ZZEF1(D1850N)",null,null,"zinc finger region (ZZ-type 2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs561018118",7.5642965204236008E-4,{"$nulls":6},"p.Asp1850Asn","c.5548G>A","MODERATE","1850/2961",35,1,{"$nulls":4},"5","486","356","326","238","401","306","0","0","0","0.5719",{"$nulls":20},"2.881491","-2.88","1.485","0.99949","-1.65","0.897","0.015","0.544",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":7},"0/0","456,0","0","456","0/1","154,192","0.5549","346",null,"chr17:4052023:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5546"]
["04HS","T10","JLPIKTOR_JLPIKTOR_17113004HS","ZZEF1","chr17:4052023","ZZEF1(D1850N)",null,null,"zinc finger region (ZZ-type 2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs561018118",7.5642965204236008E-4,{"$nulls":6},"p.Asp1850Asn","c.5548G>A","MODERATE","1850/2961",35,1,{"$nulls":4},"5","486","405","326","284","405","341","0","0","0","0.6481",{"$nulls":20},"2.881491","-2.88","1.485","0.99949","-1.65","0.897","0.015","0.544",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":7},"0/0","445,0","0","445","0/1","145,240","0.6234","385",null,"chr17:4052023:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113004HS","somatic","somatic","JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113004HS/somatic/JLPIKTOR_17113004HS_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113004HS_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6268"]

{"sheet":"05PG","index":3,"n_rows":114,"n_cols":107,"rows_kept":114}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ABCA4","chr1:94001994","ABCA4(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Fundus flavimaculatus (FFM) [MIM:248200]: Autosomal recessive retinal disorder very similar to Stargardt disease. In contrast to Stargardt disease, FFM is characterized by later onset and slowly progressive course. {ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:9781034}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Macular degeneration, age-related, 2 (ARMD2) [MIM:153800]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269|PubMed:19028736, ECO:0000269|PubMed:9295268}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Cone-rod dystrophy 3 (CORD3) [MIM:604116]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:10958761, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:11527935}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 19 (RP19) [MIM:601718]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP19 is characterized by choroidal atrophy. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: In the visual cycle, acts as an inward-directed retinoid flipase, retinoid substrates imported by ABCA4 from the extracellular or intradiscal (rod) membrane surfaces to the cytoplasmic membrane surface are all-trans-retinaldehyde (ATR) and N-retinyl-phosphatidyl-ethanolamine (NR-PE). Once transported to the cytoplasmic surface, ATR is reduced to vitamin A by trans- retinol dehydrogenase (tRDH) and then transferred to the retinal pigment epithelium (RPE) where it is converted to 11-cis-retinal. May play a role in photoresponse, removing ATR/NR-PE from the extracellular photoreceptor surfaces during bleach recovery. {ECO:0000269|PubMed:10075733}.; ",{"$nulls":5},"c.6148-2A>T","HIGH",null,44,{"$nulls":5},"4","479","487","323","323","452","458","0","0","0","0.0808",{"$nulls":5},"(ABCA4|ENSG00000198691|1|1.00)",{"$nulls":14},"6.2104",null,null,"1",{"$nulls":7},"Unknown",-1,"AR","Cone-rod dystrophy 3; Retinitis pigmentosa 19; Stargardt disease 1; Retinal dystrophy, early-onset severe; Fundus flavimaculatus","Ophthalmologic",{"$nulls":3},"C3495438| C1855465| C1858806| C1866422","0/0","471,0","0","471","0/1","436,38","0.0802","474",null,"chr1:94001994:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0898"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ABCA4","chr1:94001994","ABCA4(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Fundus flavimaculatus (FFM) [MIM:248200]: Autosomal recessive retinal disorder very similar to Stargardt disease. In contrast to Stargardt disease, FFM is characterized by later onset and slowly progressive course. {ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:9781034}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Macular degeneration, age-related, 2 (ARMD2) [MIM:153800]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269|PubMed:19028736, ECO:0000269|PubMed:9295268}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Cone-rod dystrophy 3 (CORD3) [MIM:604116]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:10958761, ECO:0000269|PubMed:11385708, ECO:0000269|PubMed:11527935}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 19 (RP19) [MIM:601718]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP19 is characterized by choroidal atrophy. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: In the visual cycle, acts as an inward-directed retinoid flipase, retinoid substrates imported by ABCA4 from the extracellular or intradiscal (rod) membrane surfaces to the cytoplasmic membrane surface are all-trans-retinaldehyde (ATR) and N-retinyl-phosphatidyl-ethanolamine (NR-PE). Once transported to the cytoplasmic surface, ATR is reduced to vitamin A by trans- retinol dehydrogenase (tRDH) and then transferred to the retinal pigment epithelium (RPE) where it is converted to 11-cis-retinal. May play a role in photoresponse, removing ATR/NR-PE from the extracellular photoreceptor surfaces during bleach recovery. {ECO:0000269|PubMed:10075733}.; ",{"$nulls":5},"c.6148-2A>T","HIGH",null,44,{"$nulls":5},"4","479","418","323","279","454","392","0","0","0","0.1888",{"$nulls":5},"(ABCA4|ENSG00000198691|1|1.00)",{"$nulls":14},"6.2104",null,null,"1",{"$nulls":7},"Unknown",-1,"AR","Cone-rod dystrophy 3; Retinitis pigmentosa 19; Stargardt disease 1; Retinal dystrophy, early-onset severe; Fundus flavimaculatus","Ophthalmologic",{"$nulls":3},"C3495438| C1855465| C1858806| C1866422","0/0","469,0","0","469","0/1","329,75","0.1856","404",null,"chr1:94001994:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1756"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ADAM10","chr15:58611934","ADAM10(K523fs)",null,null,"topological domain (Extracellular ), domain (Disintegrin ), disulfide bond , strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Reticulate acropigmentation of Kitamura (RAK) [MIM:615537]: A rare cutaneous pigmentation disorder characterized by reticulate, slightly depressed, sharply demarcated brown macules without hypopigmentation, affecting the dorsa of the hands and feet and appearing in the first or second decade of life. The macules gradually darken and extend to the proximal regions of the extremities. The manifestations tend to progress until middle age, after which progression of the eruptions stops. The pigmentary augmentation is found on the flexor aspects of the wrists, neck, patella and olecranon. Other features include breaks in the epidermal ridges on the palms and fingers, palmoplantar pits, occasionally plantar keratoderma, and partial alopecia. {ECO:0000269|PubMed:23666529}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Alzheimer disease 18 (AD18) [MIM:615590]: A late-onset form of Alzheimer disease. Alzheimer disease is a neurodegenerative disorder characterized by progressive dementia, loss of cognitive abilities, and deposition of fibrillar amyloid proteins as intraneuronal neurofibrillary tangles, extracellular amyloid plaques and vascular amyloid deposits. The major constituents of these plaques are neurotoxic amyloid-beta protein 40 and amyloid-beta protein 42, that are produced by the proteolysis of the transmembrane APP protein. The cytotoxic C- terminal fragments (CTFs) and the caspase-cleaved products, such as C31, are also implicated in neuronal death. {ECO:0000269|PubMed:19608551, ECO:0000269|PubMed:24055016}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Cleaves the membrane-bound precursor of TNF-alpha at '76-Ala-|-Val-77' to its mature soluble form. Responsible for the proteolytical release of soluble JAM3 from endothelial cells surface (PubMed:20592283). Responsible for the proteolytic release of several other cell-surface proteins, including heparin-binding epidermal growth-like factor, ephrin-A2, CD44, CDH2 and for constitutive and regulated alpha-secretase cleavage of amyloid precursor protein (APP) (PubMed:26686862, PubMed:11786905, PubMed:29224781). Contributes to the normal cleavage of the cellular prion protein (PubMed:11477090). Involved in the cleavage of the adhesion molecule L1 at the cell surface and in released membrane vesicles, suggesting a vesicle-based protease activity (PubMed:12475894). Controls also the proteolytic processing of Notch and mediates lateral inhibition during neurogenesis (By similarity). Responsible for the FasL ectodomain shedding and for the generation of the remnant ADAM10-processed FasL (FasL APL) transmembrane form (PubMed:17557115). Also cleaves the ectodomain of the integral membrane proteins CORIN and ITM2B (PubMed:19114711, PubMed:21288900). May regulate the EFNA5-EPHA3 signaling (PubMed:16239146). {ECO:0000250|UniProtKB:O35598, ECO:0000269|PubMed:11477090, ECO:0000269|PubMed:11786905, ECO:0000269|PubMed:12475894, ECO:0000269|PubMed:16239146, ECO:0000269|PubMed:17557115, ECO:0000269|PubMed:19114711, ECO:0000269|PubMed:20592283, ECO:0000269|PubMed:21288900, ECO:0000269|PubMed:26686862, ECO:0000269|PubMed:29224781}.; ",{"$nulls":4},"p.Lys523fs","c.1568delA","HIGH","523/748",12,{"$nulls":5},"4","517","465","328","288","422","368","0","0","0","0.125",{"$nulls":5},"(ADAM10|ENSG00000137845|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Reticulate acropigmentation of Kitamura","Dermatologic",{"$nulls":3},"C0406811| C3810041","0/0","489,0","0","489","0/1","365,61","0.1432","426",null,"chr15:58611934:CT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1354"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ADAM19","chr5:157491724","ADAM19(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Participates in the proteolytic processing of beta-type neuregulin isoforms which are involved in neurogenesis and synaptogenesis, suggesting a regulatory role in glial cell. Also cleaves alpha-2 macroglobulin. May be involved in osteoblast differentiation and/or osteoblast activity in bone (By similarity). {ECO:0000250}.; ",{"$nulls":5},"c.1987-1G>C","HIGH",null,17,{"$nulls":5},"5","763","627","614","483","657","529","0","0","0","0.1096",{"$nulls":5},"(ADAM19|ENSG00000135074|1|1.00)",{"$nulls":14},"5.124777",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","756,0","0","756","0/1","554,62","0.1006","616",null,"chr5:157491724:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1097"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ADAM19","chr5:157491724","ADAM19(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Participates in the proteolytic processing of beta-type neuregulin isoforms which are involved in neurogenesis and synaptogenesis, suggesting a regulatory role in glial cell. Also cleaves alpha-2 macroglobulin. May be involved in osteoblast differentiation and/or osteoblast activity in bone (By similarity). {ECO:0000250}.; ",{"$nulls":5},"c.1987-1G>C","HIGH",null,17,{"$nulls":5},"5","763","510","614","404","658","430","0","0","0","0.1814",{"$nulls":5},"(ADAM19|ENSG00000135074|1|1.00)",{"$nulls":14},"5.124777",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","758,0","0","758","0/1","400,92","0.187","492",null,"chr5:157491724:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1782"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","AIM1L","chr1:26328749","AIM1L(R1480P)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg1480Pro","c.4439G>C","MODERATE","1480/1661",16,{"$nulls":5},"4","547","479","407","353",null,null,"0","0",{"$nulls":22},"2.931465",null,null,"0.997806;0.997806;1",{"$nulls":3},".;0.855;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","526,0","0","526","0/1","433,24","0.0525","457",null,"chr1:26328749:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0567"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","AIM1L","chr1:26328749","AIM1L(R1480P)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg1480Pro","c.4439G>C","MODERATE","1480/1661",16,{"$nulls":5},"5","547","497","407","354","432","378","0","0","0","0.1693",{"$nulls":20},"2.931465",null,null,"0.997806;0.997806;1",{"$nulls":3},".;0.855;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","518,0","0","518","0/1","379,81","0.1761","460",null,"chr1:26328749:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1497"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ASXL1","chr20:32358813","ASXL1(W13*)",null,null,"domain (HTH HARE-type )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Bohring-Opitz syndrome (BOPS) [MIM:605039]: A syndrome characterized by severe intrauterine growth retardation, poor feeding, profound mental retardation, trigonocephaly, prominent metopic suture, exophthalmos, nevus flammeus of the face, upslanting palpebral fissures, hirsutism, and flexion of the elbows and wrists with deviation of the wrists and metacarpophalangeal joints. {ECO:0000269|PubMed:21706002}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myelodysplastic syndrome (MDS) [MIM:614286]: A heterogeneous group of closely related clonal hematopoietic disorders. All are characterized by a hypercellular or hypocellular bone marrow with impaired morphology and maturation, dysplasia of the myeloid, megakaryocytic and/or erythroid lineages, and peripheral blood cytopenias resulting from ineffective blood cell production. Included diseases are: refractory anemia (RA), refractory anemia with ringed sideroblasts (RARS), refractory anemia with excess blasts (RAEB), refractory cytopenia with multilineage dysplasia and ringed sideroblasts (RCMD-RS); chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative disease. MDS is considered a premalignant condition in a subgroup of patients that often progresses to acute myeloid leukemia (AML). {ECO:0000269|PubMed:19388938, ECO:0000269|PubMed:20182461}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Probable Polycomb group (PcG) protein involved in transcriptional regulation mediated by ligand-bound nuclear hormone receptors, such as retinoic acid receptors (RARs) and peroxisome proliferator-activated receptor gamma (PPARG). Acts as coactivator of RARA and RXRA through association with NCOA1. Acts as corepressor for PPARG and suppresses its adipocyte differentiation-inducing activity (By similarity). Non-catalytic component of the PR-DUB complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-119' (H2AK119ub1). {ECO:0000250, ECO:0000269|PubMed:16606617, ECO:0000269|PubMed:20436459}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Trp13*","c.38G>A","HIGH","13/1541",1,{"$nulls":5},"4","62","52","44","33","59","45","0","0","0","0.1111",{"$nulls":5},"(ASXL1|ENSG00000171456|1|1.00)","(ASXL1|ENSG00000171456|1|1.00)",{"$nulls":13},"7.6891739999999995",null,null,"1",{"$nulls":3},"0.527;0.603;0.527;.;0.544",{"$nulls":3},"Unknown",-1,"AD","Bohring-Opitz syndrome","Craniofacial; Dermatologic; Musculoskeletal; Neurologic","COSMIC",null,null,"C0796232| C3463824","0/0","63,0","0","63","0/1","43,5","0.1042","48",null,"chr20:32358813:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1515"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","BBS1","chr11:66523850","BBS1(Splicing Acceptor/Donor Loss)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Bardet-Biedl syndrome 1 (BBS1) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:12118255, ECO:0000269|PubMed:12524598, ECO:0000269|PubMed:12567324, ECO:0000269|PubMed:12677556, ECO:0000269|PubMed:12920096, ECO:0000269|PubMed:15770229, ECO:0000269|PubMed:21052717, ECO:0000269|PubMed:21344540}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for proper BBSome complex assembly and its ciliary localization (PubMed:17574030, PubMed:22072986). Plays a role in olfactory cilium biogenesis/maintenance and trafficking (By similarity). {ECO:0000250|UniProtKB:Q3V3N7, ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.; ",{"$nulls":4},"p.Lys361_Pro370del","c.1081_1110+27delAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCCAC","HIGH","361/593",11,{"$nulls":20},"66523907",{"$nulls":26},"Unknown",-1,"AR ","Bardet-Biedl syndrome 1","Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C2936862| C0752166",{"$nulls":9},"chr11:66523850:GACAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","BBS1","chr11:66523850","BBS1(Splicing Acceptor/Donor Loss)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Bardet-Biedl syndrome 1 (BBS1) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:12118255, ECO:0000269|PubMed:12524598, ECO:0000269|PubMed:12567324, ECO:0000269|PubMed:12677556, ECO:0000269|PubMed:12920096, ECO:0000269|PubMed:15770229, ECO:0000269|PubMed:21052717, ECO:0000269|PubMed:21344540}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for proper BBSome complex assembly and its ciliary localization (PubMed:17574030, PubMed:22072986). Plays a role in olfactory cilium biogenesis/maintenance and trafficking (By similarity). {ECO:0000250|UniProtKB:Q3V3N7, ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.; ",{"$nulls":4},"p.Lys361_Pro370del","c.1081_1110+27delAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCCAC","HIGH","361/593",11,{"$nulls":5},"3",null,null,"381","250","274","211",null,null,"0","0.1374",{"$nulls":5},"(BBS1|ENSG00000174483|1|1.00),(AP002748.5|ENSG00000256349|1|1.00)",{"$nulls":25},"Unknown",-1,"AR ","Bardet-Biedl syndrome 1","Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C2936862| C0752166","0/0","604,0","0","604","0/1","403,35","0.0799","438",null,"chr11:66523850:GACAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.096"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","BBS1","chr11:66523850","BBS1(Splicing Acceptor/Donor Loss)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Bardet-Biedl syndrome 1 (BBS1) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:12118255, ECO:0000269|PubMed:12524598, ECO:0000269|PubMed:12567324, ECO:0000269|PubMed:12677556, ECO:0000269|PubMed:12920096, ECO:0000269|PubMed:15770229, ECO:0000269|PubMed:21052717, ECO:0000269|PubMed:21344540}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for proper BBSome complex assembly and its ciliary localization (PubMed:17574030, PubMed:22072986). Plays a role in olfactory cilium biogenesis/maintenance and trafficking (By similarity). {ECO:0000250|UniProtKB:Q3V3N7, ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.; ",{"$nulls":4},"p.Lys361_Pro370del","c.1081_1110+27delAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCCAC","HIGH","361/593",11,{"$nulls":20},"66523907",{"$nulls":26},"Unknown",-1,"AR ","Bardet-Biedl syndrome 1","Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C2936862| C0752166",{"$nulls":9},"chr11:66523850:GACAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","BBS1","chr11:66523850","BBS1(Splicing Acceptor/Donor Loss)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Bardet-Biedl syndrome 1 (BBS1) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:12118255, ECO:0000269|PubMed:12524598, ECO:0000269|PubMed:12567324, ECO:0000269|PubMed:12677556, ECO:0000269|PubMed:12920096, ECO:0000269|PubMed:15770229, ECO:0000269|PubMed:21052717, ECO:0000269|PubMed:21344540}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for proper BBSome complex assembly and its ciliary localization (PubMed:17574030, PubMed:22072986). Plays a role in olfactory cilium biogenesis/maintenance and trafficking (By similarity). {ECO:0000250|UniProtKB:Q3V3N7, ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.; ",{"$nulls":4},"p.Lys361_Pro370del","c.1081_1110+27delAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCCAC","HIGH","361/593",11,{"$nulls":5},"4",null,null,"381","244","274","216",null,null,"0","0.287",{"$nulls":5},"(BBS1|ENSG00000174483|1|1.00),(AP002748.5|ENSG00000256349|1|1.00)",{"$nulls":25},"Unknown",-1,"AR ","Bardet-Biedl syndrome 1","Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C2936862| C0752166","0/0","604,0","0","604","0/1","336,70","0.1724","406",null,"chr11:66523850:GACAAGGCCCTGCTCAATGTCATCCACACCCCGGTGAGCCCCATCTCCGGCATCTGCC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1967"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","C5orf42","chr5:37247640","C5orf42(P20L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro20Leu","c.59C>T","MODERATE","20/3197",2,{"$nulls":5},"5","444","439","290","302","394","375","0","0","0","0.0853",{"$nulls":20},"4.067074","1.63",null,"0.999998;0.999998;1","-5.42",null,"0.002","0.716;0.69",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","437,0","0","437","0/1","388,40","0.0935","428",null,"chr5:37247640:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.096"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","C5orf42","chr5:37247640","C5orf42(P20L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro20Leu","c.59C>T","MODERATE","20/3197",2,{"$nulls":5},"5","444","344","290","230","395","294","0","0","0","0.3503",{"$nulls":20},"4.067074","1.63",null,"0.999998;0.999998;1","-5.42",null,"0.002","0.716;0.69",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","441,0","0","441","0/1","208,127","0.3791","335",null,"chr5:37247640:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3783"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","CAMSAP1","chr9:135866512","CAMSAP1(T204A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19508979, PubMed:21834987, PubMed:24486153, PubMed:24706919, PubMed:24117850). Specifically recognizes growing microtubule minus-ends and stabilizes microtubules (PubMed:24486153, PubMed:24706919). Acts on free microtubule minus-ends that are not capped by microtubule- nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153, PubMed:24706919). In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (- TIP) that dissociates from microtubules after allowing tubulin incorporation (PubMed:24486153, PubMed:24706919). Through interaction with spectrin may regulate neurite outgrowth (PubMed:24117850). {ECO:0000269|PubMed:19508979, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24117850, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:24706919}.; ",{"$nulls":4},"p.Thr204Ala","c.610A>G","MODERATE","204/1613",4,{"$nulls":5},"5","193","178","140","120","178","161","0","0","0","0.0807",{"$nulls":20},"2.615439","2.48","0.805","0.98721;0.98721;1","-1.1","0.687;0.36","0.304;0.228","0.309;0.32",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","193,0","0","193","0/1","162,14","0.0795","176",null,"chr9:135866512:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0833"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","CAMSAP1","chr9:135866512","CAMSAP1(T204A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19508979, PubMed:21834987, PubMed:24486153, PubMed:24706919, PubMed:24117850). Specifically recognizes growing microtubule minus-ends and stabilizes microtubules (PubMed:24486153, PubMed:24706919). Acts on free microtubule minus-ends that are not capped by microtubule- nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153, PubMed:24706919). In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (- TIP) that dissociates from microtubules after allowing tubulin incorporation (PubMed:24486153, PubMed:24706919). Through interaction with spectrin may regulate neurite outgrowth (PubMed:24117850). {ECO:0000269|PubMed:19508979, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24117850, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:24706919}.; ",{"$nulls":4},"p.Thr204Ala","c.610A>G","MODERATE","204/1613",4,{"$nulls":5},"5","193","104","140","71","178","94","0","0","0","0.1702",{"$nulls":20},"2.615439","2.48","0.805","0.98721;0.98721;1","-1.1","0.687;0.36","0.304;0.228","0.309;0.32",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","192,0","0","192","0/1","85,19","0.1827","104",null,"chr9:135866512:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.169"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","CD300E","chr17:74612747","CD300E(L175Q)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably acts as an activating receptor. {ECO:0000269|PubMed:15557162}.; ",{"$nulls":4},"p.Leu175Gln","c.524T>A","MODERATE","175/205",4,{"$nulls":5},"5","430","255","302","168","374","228","0","0","0","0.193",{"$nulls":20},"1.885812",null,"1.215","0.995689;0.996608;0.992434",null,"0.966",null,"0.403",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","416,0","0","416","0/1","201,49","0.196","250",null,"chr17:74612747:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1964"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","COL9A3","chr20:62817068","COL9A3(A2fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Multiple epiphyseal dysplasia 3 (EDM3) [MIM:600969]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. {ECO:0000269|PubMed:10090888, ECO:0000269|PubMed:25381065}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Intervertebral disc disease (IDD) [MIM:603932]: A common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. {ECO:0000269|PubMed:11308397, ECO:0000269|PubMed:25381065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Susceptibility to intervertebral disk disease is conferred by variant p.Arg103Trp (PubMed:11308397). {ECO:0000269|PubMed:11308397}.; ","FUNCTION: Structural component of hyaline cartilage and vitreous of the eye.; ",{"$nulls":4},"p.Ala2fs","c.5_17delCCGGGCCGCGCGC","HIGH","2/684",1,{"$nulls":5},"3",{"$nulls":4},"159","131",null,null,"0","0.0992",{"$nulls":31},"Unknown",-1,"AD","Epiphyseal dysplasia, multiple, 3","Musculoskeletal",{"$nulls":3},"C1832998| C0158252","0/0","177,0","0","184","0/1","126,14","0.1","149",null,"chr20:62817068:GCCGGGCCGCGCGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","COL9A3","chr20:62817083","COL9A3(C7G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Multiple epiphyseal dysplasia 3 (EDM3) [MIM:600969]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. {ECO:0000269|PubMed:10090888, ECO:0000269|PubMed:25381065}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Intervertebral disc disease (IDD) [MIM:603932]: A common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. {ECO:0000269|PubMed:11308397, ECO:0000269|PubMed:25381065}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Susceptibility to intervertebral disk disease is conferred by variant p.Arg103Trp (PubMed:11308397). {ECO:0000269|PubMed:11308397}.; ","FUNCTION: Structural component of hyaline cartilage and vitreous of the eye.; ",{"$nulls":4},"p.Cys7Gly","c.19T>G","MODERATE","7/684",1,{"$nulls":5},"3",{"$nulls":4},"152","125",null,null,"0","0.104",{"$nulls":20},"0.169093",".;-2.67","-0.65","1",".;0.21","0.0",".;0.508",".;0.122",{"$nulls":3},"Unknown",-1,"AD","Epiphyseal dysplasia, multiple, 3","Musculoskeletal",{"$nulls":3},"C1832998| C0158252","0/0","184,1","0.0054","191","0/1","137,16","0.1046","156",null,"chr20:62817083:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","CTTNBP2","chr7:117810811","CTTNBP2(E123G)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulates the dendritic spine distribution of CTTN/cortactin in hippocampal neurons, thus controls dendritic spinogenesis and dendritic spine maintenance. {ECO:0000250}.; ",{"$nulls":4},"p.Glu123Gly","c.368A>G","MODERATE","123/1663",3,{"$nulls":5},"4","422","342",null,null,"324","261","0","0","0","0.0766",{"$nulls":20},"4.110896","0.86","1.76;.;.;.","0.999764","-4.4;-5.2;-5.49;-5.57","0.972;.;.;.","0.002;0.179;0.306;0.02","0.636;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein with six ankyrin repeats and several proline-rich regions. A similar gene in rat interacts with a central regulator of the actin cytoskeleton. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","408,0","0","408","0/1","311,25","0.0744","336",null,"chr7:117810811:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","DNAH7","chr2:195906966","DNAH7(N1383S)",null,null,"region of interest (AAA 1 ), splice variant (In isoform 2. ), splice variant (In isoform 3. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asn1383Ser","c.4148A>G","MODERATE","1383/4024",26,{"$nulls":5},"5","435","372","298","271","404","340","0","0","0","0.1324",{"$nulls":20},"3.746556","0.92","4.38","1","-4.89","1.0","0.002","0.831",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","425,0","0","425","0/1","311,53","0.1456","364",null,"chr2:195906966:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1439"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","DRD4","chr11:640410","DRD4(L356P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Dopamine receptor responsible for neuronal signaling in the mesolimbic system of the brain, an area of the brain that regulates emotion and complex behavior. Activated by dopamine, but also by epinephrine and norepinephrine, and by numerous synthetic agonists and drugs (PubMed:9003072, PubMed:16423344, PubMed:27659709, PubMed:29051383). Agonist binding triggers signaling via G proteins that inhibit adenylyl cyclase (PubMed:7512953, PubMed:7643093, PubMed:16423344, PubMed:27659709, PubMed:29051383). Modulates the circadian rhythm of contrast sensitivity by regulating the rhythmic expression of NPAS2 in the retinal ganglion cells (By similarity). {ECO:0000250|UniProtKB:P51436, ECO:0000269|PubMed:16423344, ECO:0000269|PubMed:1840645, ECO:0000269|PubMed:27659709, ECO:0000269|PubMed:29051383, ECO:0000269|PubMed:7512953, ECO:0000269|PubMed:7643093, ECO:0000269|PubMed:8078498, ECO:0000269|PubMed:9003072}.; ",{"$nulls":4},"p.Leu356Pro","c.1067T>C","MODERATE","356/419",4,{"$nulls":5},"3",null,null,"232","165","215","155",null,null,"0","0.0774",{"$nulls":20},"4.652279","-0.75",null,"1","-5.12",null,null,"0.783",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes the D4 subtype of the dopamine receptor. The D4 subtype is a G-protein coupled receptor which inhibits adenylyl cyclase. It is a target for drugs which treat schizophrenia and Parkinson disease. Mutations in this gene have been associated with various behavioral phenotypes, including autonomic nervous system dysfunction, attention deficit/hyperactivity disorder, and the personality trait of novelty seeking. This gene contains a polymorphic number (2-10 copies) of tandem 48 nt repeats; the sequence shown contains four repeats. [provided by RefSeq, Jul 2008].  ",null,"C1263846","0/0","273,0","0","275","0/1","180,12","0.0625","193",null,"chr11:640410:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0667"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ELFN1","chr7:1746905","ELFN1(C770Y)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Postsynaptic protein that regulates circuit dynamics in the central nervous system by modulating the temporal dynamics of interneuron recruitment. Specifically present in excitatory synapses onto oriens-lacunosum molecular (OLM) interneurons and acts as a regulator of presynaptic release probability to direct the formation of highly facilitating pyramidal-OLM synapses (By similarity). Inhibits phosphatase activity of protein phosphatase 1 (PP1) complexes. {ECO:0000250, ECO:0000269|PubMed:19389623}.; ",{"$nulls":4},"p.Cys770Tyr","c.2309G>A","MODERATE","770/828",3,{"$nulls":5},"5","553","537","432","416","462","440","0","0","0","0.0818",{"$nulls":20},"3.437093","0.15","2.16","1","-3.34",null,"0.083","0.735;0.736",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","539,0","0","539","0/1","478,47","0.0895","525",null,"chr7:1746905:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0865"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ELFN1","chr7:1746905","ELFN1(C770Y)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Postsynaptic protein that regulates circuit dynamics in the central nervous system by modulating the temporal dynamics of interneuron recruitment. Specifically present in excitatory synapses onto oriens-lacunosum molecular (OLM) interneurons and acts as a regulator of presynaptic release probability to direct the formation of highly facilitating pyramidal-OLM synapses (By similarity). Inhibits phosphatase activity of protein phosphatase 1 (PP1) complexes. {ECO:0000250, ECO:0000269|PubMed:19389623}.; ",{"$nulls":4},"p.Cys770Tyr","c.2309G>A","MODERATE","770/828",3,{"$nulls":5},"5","553","645","432","510","459","546","0","0","0","0.1081",{"$nulls":20},"3.437093","0.15","2.16","1","-3.34",null,"0.083","0.735;0.736",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","535,0","0","535","0/1","552,74","0.1182","626",null,"chr7:1746905:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1098"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","EXT2","chr11:44114205","EXT2(G249V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Potocki-Shaffer syndrome (POSHS) [MIM:601224]: A syndrome characterized by foramina parietalia permagna, multiple exostoses, and craniofacial dysostosis and mental retardation in some cases. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Seizures, scoliosis, and macrocephaly syndrome (SSMS) [MIM:616682]: An autosomal recessive syndrome characterized by seizures, intellectual disability, hypotonia, scoliosis, macrocephaly, hypertelorism and renal dysfunction. {ECO:0000269|PubMed:26246518}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Appears to be a tumor suppressor. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:22660413}.; ","gedi|level2",{"$nulls":3},"p.Gly249Val","c.746G>T","MODERATE","249/751",4,{"$nulls":5},"4","512","458","396","345","443","383","0","0","0","0.0653",{"$nulls":20},"4.175663","-4.6","2.915;2.915;.;2.915","1","-6.53;-6.53;-6.58;-6.53","1.0;1.0;.;1.0","0.001","0.909;0.789;0.9;0.91",{"$nulls":3},"Unknown",-1,"AD","Exostoses, multiple, type 2","Musculoskeletal; Oncologic","COSMIC,vGLI","This gene encodes one of two glycosyltransferases involved in the chain elongation step of heparan sulfate biosynthesis. Mutations in this gene cause the type II form of multiple exostoses. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008].",null,"C1851413| C4225248","0/0","496,0","0","496","0/1","407,26","0.06","433",null,"chr11:44114205:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0609"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","EXT2","chr11:44114205","EXT2(G249V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Potocki-Shaffer syndrome (POSHS) [MIM:601224]: A syndrome characterized by foramina parietalia permagna, multiple exostoses, and craniofacial dysostosis and mental retardation in some cases. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Seizures, scoliosis, and macrocephaly syndrome (SSMS) [MIM:616682]: An autosomal recessive syndrome characterized by seizures, intellectual disability, hypotonia, scoliosis, macrocephaly, hypertelorism and renal dysfunction. {ECO:0000269|PubMed:26246518}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Glycosyltransferase required for the biosynthesis of heparan-sulfate. The EXT1/EXT2 complex possesses substantially higher glycosyltransferase activity than EXT1 or EXT2 alone. Appears to be a tumor suppressor. Required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:22660413}.; ","gedi|level2",{"$nulls":3},"p.Gly249Val","c.746G>T","MODERATE","249/751",4,{"$nulls":5},"4","512","391","396","299","443","339","0","0","0","0.1829",{"$nulls":20},"4.175663","-4.6","2.915;2.915;.;2.915","1","-6.53;-6.53;-6.58;-6.53","1.0;1.0;.;1.0","0.001","0.909;0.789;0.9;0.91",{"$nulls":3},"Unknown",-1,"AD","Exostoses, multiple, type 2","Musculoskeletal; Oncologic","COSMIC,vGLI","This gene encodes one of two glycosyltransferases involved in the chain elongation step of heparan sulfate biosynthesis. Mutations in this gene cause the type II form of multiple exostoses. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008].",null,"C1851413| C4225248","0/0","495,0","0","495","0/1","304,62","0.1694","366",null,"chr11:44114205:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1572"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","FSIP2","chr2:185800308","FSIP2(F3757V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Phe3757Val","c.11269T>G","MODERATE","3757/6996",17,{"$nulls":5},"5","229","179","179","148","186","141","0","0","0","0.0567",{"$nulls":20},"0.012937","1.16","-0.55","1","1.0",null,"1.0","0.088",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748403","0/0","230,0","0","230","0/1","167,10","0.0565","177",null,"chr2:185800308:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0676"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","GNMT","chr6:42962228","GNMT(L75M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the methylation of glycine by using S- adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine. {ECO:0000269|PubMed:15340920, ECO:0000269|PubMed:17660255}.; ",{"$nulls":4},"p.Leu75Met","c.223C>A","MODERATE","75/295",2,{"$nulls":5},"5","812","688","616","493","666","586","0","0","0","0.0597",{"$nulls":20},"3.642669","-1.12","2.125","0.999836","-1.94","1.0","0.003","0.625",{"$nulls":3},"Unknown",-1,"AR","Glycine N-methyltransferase deficiency","Biochemical; Gastrointestinal",{"$nulls":3},"C1847720","0/0","803,0","0","803","0/1","634,41","0.0607","675",null,"chr6:42962228:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0649"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","GNMT","chr6:42962228","GNMT(L75M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the methylation of glycine by using S- adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine. {ECO:0000269|PubMed:15340920, ECO:0000269|PubMed:17660255}.; ",{"$nulls":4},"p.Leu75Met","c.223C>A","MODERATE","75/295",2,{"$nulls":5},"5","812","801","616","602","667","660","0","0","0","0.1561",{"$nulls":20},"3.642669","-1.12","2.125","0.999836","-1.94","1.0","0.003","0.625",{"$nulls":3},"Unknown",-1,"AR","Glycine N-methyltransferase deficiency","Biochemical; Gastrointestinal",{"$nulls":3},"C1847720","0/0","790,0","0","790","0/1","660,122","0.156","782",null,"chr6:42962228:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1678"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","GRXCR2","chr5:145866692","GRXCR2(Y125N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Deafness, autosomal recessive, 101 (DFNB101) [MIM:615837]: A form of non-syndromic deafness characterized by bilateral, moderate to severe hearing loss. Vestibular function is unaffected. {ECO:0000269|PubMed:24619944}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Could play a role in maintaining cochlear stereocilia bundles that are involved in sound detection. {ECO:0000269|PubMed:24619944}.; ",{"$nulls":4},"p.Tyr125Asn","c.373T>A","MODERATE","125/248",2,{"$nulls":5},"3","279","144","179","102",null,null,"0","0",{"$nulls":22},"4.039264","1.85","3.115","1","-7.7","1.0",{"$nulls":5},"Unknown",-1,"AR","Deafness, autosomal recessive 101","Audiologic/Otolaryngologic",{"$nulls":3},"C3892049","0/0","273,0","0","273","0/1","131,8","0.0576","139",null,"chr5:145866692:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0686"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","HIST1H2AG","chr6:27133065","HIST1H2AG(start_lost)",{"$nulls":3},"initiator-methionine:Removed, modified-residue:N-acetylserine, modified-residue:Phosphoserine, modified-residue:N6-acetyllysine, modified-residue:Citrulline, modified-residue:Symmetric_dimethylarginine","MODERATE, MODERATE, MODERATE, MODERATE, LOW, LOW",null,255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.; ",{"$nulls":4},"p.Met1_Gly9del","c.-6_27delCTCGCTATGTCTGGACGTGGCAAGCAGGGAGGC","HIGH","1/130",1,{"$nulls":5},"4","1274","1105","975","847","1290","1070","0","0","0","0.1112",{"$nulls":5},"(HIST1H2AG|ENSG00000196787|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","1680,0","0","1680","0/1","1198,113","0.0862","1311",null,"chr6:27133065:GCTCGCTATGTCTGGACGTGGCAAGCAGGGAGGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1358"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","HTR2C","chrX:114907350","HTR2C(V438I)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for various drugs and psychoactive substances, including ergot alkaloid derivatives, 1- 2,5,-dimethoxy-4-iodophenyl-2-aminopropane (DOI) and lysergic acid diethylamide (LSD). Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Beta-arrestin family members inhibit signaling via G proteins and mediate activation of alternative signaling pathways. Signaling activates a phosphatidylinositol-calcium second messenger system that modulates the activity of phosphatidylinositol 3-kinase and down-stream signaling cascades and promotes the release of Ca(2+) ions from intracellular stores. Regulates neuronal activity via the activation of short transient receptor potential calcium channels in the brain, and thereby modulates the activation of pro-opiomelacortin neurons and the release of CRH that then regulates the release of corticosterone. Plays a role in the regulation of appetite and eating behavior, responses to anxiogenic stimuli and stress. Plays a role in insulin sensitivity and glucose homeostasis. {ECO:0000269|PubMed:12970106, ECO:0000269|PubMed:18703043, ECO:0000269|PubMed:19057895, ECO:0000269|PubMed:7895773}.; ",{"$nulls":4},"p.Val438Ile","c.1312G>A","MODERATE","438/458",6,{"$nulls":5},"5","396","366","261","276","354","352","0","0","0","0.0568",{"$nulls":20},"0.934933","0.34",null,"1","-0.01",null,"0.226","0.035;0.041",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","386,0","0","386","0/1","345,23","0.0625","368",null,"chrX:114907350:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0652"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","HTR2C","chrX:114907350","HTR2C(V438I)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for various drugs and psychoactive substances, including ergot alkaloid derivatives, 1- 2,5,-dimethoxy-4-iodophenyl-2-aminopropane (DOI) and lysergic acid diethylamide (LSD). Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Beta-arrestin family members inhibit signaling via G proteins and mediate activation of alternative signaling pathways. Signaling activates a phosphatidylinositol-calcium second messenger system that modulates the activity of phosphatidylinositol 3-kinase and down-stream signaling cascades and promotes the release of Ca(2+) ions from intracellular stores. Regulates neuronal activity via the activation of short transient receptor potential calcium channels in the brain, and thereby modulates the activation of pro-opiomelacortin neurons and the release of CRH that then regulates the release of corticosterone. Plays a role in the regulation of appetite and eating behavior, responses to anxiogenic stimuli and stress. Plays a role in insulin sensitivity and glucose homeostasis. {ECO:0000269|PubMed:12970106, ECO:0000269|PubMed:18703043, ECO:0000269|PubMed:19057895, ECO:0000269|PubMed:7895773}.; ",{"$nulls":4},"p.Val438Ile","c.1312G>A","MODERATE","438/458",6,{"$nulls":5},"5","396","335","261","242","355","301","0","0","0","0.1628",{"$nulls":20},"0.934933","0.34",null,"1","-0.01",null,"0.226","0.035;0.041",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","386,0","0","386","0/1","272,59","0.1782","331",null,"chrX:114907350:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.157"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","IGF2R","chr6:160058937","IGF2R(G977A)",null,null,"topological domain (Lumenal ), domain (MRH 7 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transport of phosphorylated lysosomal enzymes from the Golgi complex and the cell surface to lysosomes. Lysosomal enzymes bearing phosphomannosyl residues bind specifically to mannose-6- phosphate receptors in the Golgi apparatus and the resulting receptor-ligand complex is transported to an acidic prelyosomal compartment where the low pH mediates the dissociation of the complex. This receptor also binds IGF2. Acts as a positive regulator of T-cell coactivation, by binding DPP4. {ECO:0000269|PubMed:10900005}.; ","gedi",{"$nulls":3},"p.Gly977Ala","c.2930G>C","MODERATE","977/2491",22,{"$nulls":5},"5","401","362","295","277","350","305","0","0","0","0.0689",{"$nulls":20},"2.59571","2.71;.",null,"0.999533","-2.43;.","1.0","0.018;.","0.46;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C2239176","0/0","398,0","0","398","0/1","331,26","0.0728","357",null,"chr6:160058937:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0758"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","IGF2R","chr6:160058937","IGF2R(G977A)",null,null,"topological domain (Lumenal ), domain (MRH 7 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transport of phosphorylated lysosomal enzymes from the Golgi complex and the cell surface to lysosomes. Lysosomal enzymes bearing phosphomannosyl residues bind specifically to mannose-6- phosphate receptors in the Golgi apparatus and the resulting receptor-ligand complex is transported to an acidic prelyosomal compartment where the low pH mediates the dissociation of the complex. This receptor also binds IGF2. Acts as a positive regulator of T-cell coactivation, by binding DPP4. {ECO:0000269|PubMed:10900005}.; ","gedi",{"$nulls":3},"p.Gly977Ala","c.2930G>C","MODERATE","977/2491",22,{"$nulls":5},"5","401","280","295","221","347","256","0","0","0","0.1367",{"$nulls":20},"2.59571","2.71;.",null,"0.999533","-2.43;.","1.0","0.018;.","0.46;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C2239176","0/0","398,0","0","398","0/1","234,38","0.1397","272",null,"chr6:160058937:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1493"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","IQGAP1","chr15:90492550","IQGAP1(I1489M)",null,null,"region of interest (C2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a crucial role in regulating the dynamics and assembly of the actin cytoskeleton. Binds to activated CDC42 but does not stimulate its GTPase activity. It associates with calmodulin. Could serve as an assembly scaffold for the organization of a multimolecular complex that would interface incoming signals to the reorganization of the actin cytoskeleton at the plasma membrane. May promote neurite outgrowth (PubMed:15695813). May play a possible role in cell cycle regulation by contributing to cell cycle progression after DNA replication arrest (PubMed:20883816). {ECO:0000269|PubMed:15695813, ECO:0000269|PubMed:20883816}.; ",{"$nulls":4},"p.Ile1489Met","c.4467T>G","MODERATE","1489/1657",35,{"$nulls":5},"4","94","93","90","85",null,null,"0","0",{"$nulls":22},"2.9048730000000003","0.05","2.75;.","0.999999","-2.47;-2.67","1.0;.","0.003","0.953;0.938",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","94,0","0","94","0/1","83,8","0.0879","91",null,"chr15:90492550:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0824"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","IQGAP1","chr15:90492550","IQGAP1(I1489M)",null,null,"region of interest (C2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a crucial role in regulating the dynamics and assembly of the actin cytoskeleton. Binds to activated CDC42 but does not stimulate its GTPase activity. It associates with calmodulin. Could serve as an assembly scaffold for the organization of a multimolecular complex that would interface incoming signals to the reorganization of the actin cytoskeleton at the plasma membrane. May promote neurite outgrowth (PubMed:15695813). May play a possible role in cell cycle regulation by contributing to cell cycle progression after DNA replication arrest (PubMed:20883816). {ECO:0000269|PubMed:15695813, ECO:0000269|PubMed:20883816}.; ",{"$nulls":4},"p.Ile1489Met","c.4467T>G","MODERATE","1489/1657",35,{"$nulls":5},"4","94","81","90","76",null,null,"0","0",{"$nulls":22},"2.9048730000000003","0.05","2.75;.","0.999999","-2.47;-2.67","1.0;.","0.003","0.953;0.938",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","94,0","0","94","0/1","68,11","0.1392","79",null,"chr15:90492550:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1447"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","KIRREL2","chr19:35860583","KIRREL2(A282T)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 3 ), disulfide bond , splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense","rs368632197",1.1627906976744188E-4,null,"FUNCTION: May regulate basal insulin secretion. {ECO:0000250|UniProtKB:Q7TSU7}.; ",{"$nulls":4},"p.Ala282Thr","c.844G>A","MODERATE","282/708",7,{"$nulls":5},"4","1216","927","911","688","1034","783","0","0","0","0.0856",{"$nulls":20},"1.804869","2.32",null,"1;0.699667;0.699667;0.699667;0.699667;0.699667",".;-0.73;-0.73;-0.73",null,".;0.219;0.238;0.17","0.266;0.24;0.203;0.183",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,{"$nulls":7},"0/0","1183,0","0","1183","0/1","831,82","0.0898","913",null,"chr19:35860583:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0945"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","KIRREL2","chr19:35860583","KIRREL2(A282T)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 3 ), disulfide bond , splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense","rs368632197",1.1627906976744188E-4,null,"FUNCTION: May regulate basal insulin secretion. {ECO:0000250|UniProtKB:Q7TSU7}.; ",{"$nulls":4},"p.Ala282Thr","c.844G>A","MODERATE","282/708",7,{"$nulls":5},"4","1216","999","911","766","1034","821","0","0","0","0.1815",{"$nulls":20},"1.804869","2.32",null,"1;0.699667;0.699667;0.699667;0.699667;0.699667",".;-0.73;-0.73;-0.73",null,".;0.219;0.238;0.17","0.266;0.24;0.203;0.183",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,{"$nulls":7},"0/0","1178,0","0","1178","0/1","784,188","0.1934","972",null,"chr19:35860583:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1971"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","KPNA7","chr7:99203215","KPNA7(V31A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions in nuclear protein import. {ECO:0000250}.; ",{"$nulls":4},"p.Val31Ala","c.92T>C","MODERATE","31/516",2,{"$nulls":5},"5","463","384","324","278","424","344","0","0","0","0.0843",{"$nulls":20},"1.61098","1.56","2.405","0.696688","-2.52","0.034","0.052","0.103",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","459,0","0","459","0/1","342,32","0.0856","374",null,"chr7:99203215:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0971"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","KPNA7","chr7:99203215","KPNA7(V31A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions in nuclear protein import. {ECO:0000250}.; ",{"$nulls":4},"p.Val31Ala","c.92T>C","MODERATE","31/516",2,{"$nulls":5},"5","463","441","324","314","424","395","0","0","0","0.1772",{"$nulls":20},"1.61098","1.56","2.405","0.696688","-2.52","0.034","0.052","0.103",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","460,0","0","460","0/1","350,78","0.1822","428",null,"chr7:99203215:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1879"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","KRT6B","chr12:52450580","KRT6B(K194R)",null,null,"domain (IF rod ), region of interest (Coil 1A )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys194Arg","c.581A>G","MODERATE","194/564",2,{"$nulls":5},"3",null,null,"2328","1619","3380","851",null,null,"0","0.168",{"$nulls":20},"4.27411","-2.61","2.97","0.989171","-2.68","1.0","0.001","0.795",{"$nulls":3},"Unknown",-1,"AD","Pachyonychia congenita 4","Dental; Dermatologic",{"$nulls":3},"C3714949","0/0","1946,0","0","1946","0/1","1187,185","0.1348","1372",null,"chr12:52450580:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1242"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","KRT6C","chr12:52472240","KRT6C(K194R)",null,null,"domain (IF rod ), region of interest (Coil 1A )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys194Arg","c.581A>G","MODERATE","194/564",2,{"$nulls":5},"3","38","39","64","54",null,null,"0","0",{"$nulls":22},"4.204665","-2.61","3.685","0.988591","-2.66","1.0","0.001","0.709",{"$nulls":3},"Unknown",-1,"AD","Palmoplantar keratoderma, nonepidermolytic, focal or diffuse","Dermatologic",{"$nulls":3},"C3810394","0/0","37,0","0","37","0/1","29,10","0.2564","39",null,"chr12:52472240:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2222"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","LRFN1","chr19:39314032","LRFN1(E432fs)",null,null,"topological domain (Extracellular ), domain (Fibronectin type-III )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Promotes neurite outgrowth in hippocampal neurons. Involved in the regulation and maintenance of excitatory synapses. Induces the clustering of excitatory postsynaptic proteins, including DLG4, DLGAP1, GRIA1 and GRIN1 (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu432fs","c.1294_1305del>GAN_EAELED<insG","HIGH","432/771",1,{"$nulls":20},"39314763",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr19:39314032:<DELETE_NUC>:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","LRRC4","chr7:128029249","LRRC4(I464M)",null,null,"topological domain (Extracellular ), compositionally biased region (Thr-rich )",{"$nulls":3},255,"PASS","Missense","rs764702274",1.156E-4,null,"FUNCTION: Synaptic adhesion protein. Regulates the formation of exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays a important role for auditory synaptic responses. Involved in the suppression of glioma (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ile464Met","c.1392C>G","MODERATE","464/653",2,{"$nulls":5},"4","1434","1171","1116","877","1230","1021","0","0","0","0.0715",{"$nulls":20},"1.5833439999999999","1.57","0.345","1;0.993224","0.4","0.001","0.18","0.266",{"$nulls":3},"ExAC_EAS_AF",1.156E-4,{"$nulls":7},"0/0","1394,0","0","1394","0/1","1043,78","0.0696","1121",null,"chr7:128029249:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0707"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","MIA3","chr1:222653124","MIA3(I1402fs)",null,null,"topological domain (Cytoplasmic ), region of interest (Mediates interaction with MIA2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Plays a role in the transport of cargos that are too large to fit into COPII-coated vesicles and require specific mechanisms to be incorporated into membrane-bound carriers and exported from the endoplasmic reticulum. This protein is required for collagen VII (COL7A1) secretion by loading COL7A1 into transport carriers. It may participate in cargo loading of COL7A1 at endoplasmic reticulum exit sites by binding to COPII coat subunits Sec23/24 and guiding SH3-bound COL7A1 into a growing carrier. Does not play a role in global protein secretion and is apparently specific to COL7A1 cargo loading. However, it may participate in secretion of other proteins in cells that do not secrete COL7A1. It is also specifically required for the secretion of lipoproteins by participating in their export from the endoplasmic reticulum (PubMed:27138255). {ECO:0000269|PubMed:19269366, ECO:0000269|PubMed:27138255}.; ",{"$nulls":4},"p.Ile1402fs","c.4206_4209delTAAT","HIGH","1402/1907",14,{"$nulls":5},"4",null,null,"194","125","188","110",null,null,"0","0.0727",{"$nulls":5},"(MIA3|ENSG00000154305|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","248,0","0","248","0/1","139,10","0.0671","149",null,"chr1:222653124:TATTA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.056"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","MIB2","chr1:1625289","MIB2(K357R)",null,null,"splice variant (In isoform 6. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of Delta receptors, which act as ligands of Notch proteins. Positively regulates the Delta-mediated Notch signaling by ubiquitinating the intracellular domain of Delta, leading to endocytosis of Delta receptors. {ECO:0000250|UniProtKB:Q8R516}.; ",{"$nulls":4},"p.Lys357Arg","c.1070A>G","MODERATE","357/1070",7,{"$nulls":5},"3","841","727",{"$nulls":4},"0.0012","0.0012",{"$nulls":22},"2.394023","1.32;1.33;1.34;1.32;-0.16;1.34;1.35",null,"0.981588;0.981588;0.981588;0.98883;0.98883;0.981588;0.981588;0.981588;0.978011;0.998338","-1.45;-1.45;-1.53;-1.45;-1.47;-1.45;-1.37",null,"0.053;0.046;0.342;0.048;0.441;0.081;0.092","0.113;0.153;0.239;0.12;0.254;0.133;0.132",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","828,1","0.0012","829","0/1","669,41","0.0577","710",null,"chr1:1625289:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","MID1IP1","chrX:38804919","MID1IP1(start_lost)",null,null,"modified residue (N-acetylmethionine )",{"$nulls":3},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Plays a role in the regulation of lipogenesis in liver. Up-regulates ACACA enzyme activity. Required for efficient lipid biosynthesis, including triacylglycerol, diacylglycerol and phospholipid. Involved in stabilization of microtubules (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met1_Lys11delinsGlu","c.-27_31delCTGCGCTCCAACGTCCGCGCGGCCACCATGATGCAAATCTGCGACACCTACAACCAGAinsG","HIGH","1/183",2,{"$nulls":20},"38804977",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chrX:38804919:CCTGCGCTCCAACGTCCGCGCGGCCACCATGATGCAAATCTGCGACACCTACAACCAGA:CG",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","MID1IP1","chrX:38804919","MID1IP1(start_lost)",null,null,"modified residue (N-acetylmethionine )",{"$nulls":3},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Plays a role in the regulation of lipogenesis in liver. Up-regulates ACACA enzyme activity. Required for efficient lipid biosynthesis, including triacylglycerol, diacylglycerol and phospholipid. Involved in stabilization of microtubules (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met1_Lys11delinsGlu","c.-27_31delCTGCGCTCCAACGTCCGCGCGGCCACCATGATGCAAATCTGCGACACCTACAACCAGAinsG","HIGH","1/183",2,{"$nulls":20},"38804977",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chrX:38804919:CCTGCGCTCCAACGTCCGCGCGGCCACCATGATGCAAATCTGCGACACCTACAACCAGA:CG",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","MLH3","chr14:75049051","MLH3(P202R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:11317354}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Probably involved in the repair of mismatches in DNA.; ","level2",{"$nulls":3},"p.Pro202Arg","c.605C>G","MODERATE","202/1453",2,{"$nulls":5},"5","684","665","542","523","603","584","0","0","0","0.0736",{"$nulls":20},"3.558638","-2.57;.;-2.57;-2.57","1.895;1.895;.;1.895","0.900688;0.900688;0.891357;0.891357;1","-4.36;.;-4.17;-4.36","0.937;0.998;.;0.937","0.119;.;0.11;0.119","0.439;0.348;0.375;0.396",{"$nulls":3},"Unknown",-1,"AD","Colorectal cancer, hereditary nonpolyposis type 7; Endometrial carcinoma","Oncologic","kMISMATCH_REPAIR",null,null,"C1858380| C1527249| C0476089","0/0","673,0","0","673","0/1","615,46","0.0696","661",null,"chr14:75049051:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0688"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","MLH3","chr14:75049051","MLH3(P202R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:11317354}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Probably involved in the repair of mismatches in DNA.; ","level2",{"$nulls":3},"p.Pro202Arg","c.605C>G","MODERATE","202/1453",2,{"$nulls":5},"5","684","598","542","463","599","526","0","0","0","0.1559",{"$nulls":20},"3.558638","-2.57;.;-2.57;-2.57","1.895;1.895;.;1.895","0.900688;0.900688;0.891357;0.891357;1","-4.36;.;-4.17;-4.36","0.937;0.998;.;0.937","0.119;.;0.11;0.119","0.439;0.348;0.375;0.396",{"$nulls":3},"Unknown",-1,"AD","Colorectal cancer, hereditary nonpolyposis type 7; Endometrial carcinoma","Oncologic","kMISMATCH_REPAIR",null,null,"C1858380| C1527249| C0476089","0/0","664,0","0","664","0/1","488,95","0.163","583",null,"chr14:75049051:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.149"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","MUC22","chr6:31029414","MUC22(A1328V)",null,null,"topological domain (Extracellular ), region of interest (124 X 10 AA approximate repeats ), compositionally biased region (Thr-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala1328Val","c.3983C>T","MODERATE","1328/1773",2,{"$nulls":5},"3","1296","948",null,null,"684","500","0.0023","0.0023","0","0.146",{"$nulls":20},"-0.308303","2.75","0.55","1","-0.55",null,"0.557","0.019",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1251,1","0.0008","1252","0/1","779,138","0.1505","917",null,"chr6:31029414:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","NAA25","chr12:112087714","NAA25(A124D)",null,null,"repeat (TPR 4 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Non-catalytic subunit of the NatB complex which catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Asp-Glu. May play a role in normal cell-cycle progression. {ECO:0000269|PubMed:18570629}.; ",{"$nulls":4},"p.Ala124Asp","c.371C>A","MODERATE","124/972",4,{"$nulls":5},"5","920","593","644","410","805","496","0","0","0","0.0605",{"$nulls":20},"4.178339","1.13","1.975","1","-3.5","1.0","0.005","0.953",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","873,0","0","873","0/1","535,37","0.0647","572",null,"chr12:112087714:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0561"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","NAA25","chr12:112087714","NAA25(A124D)",null,null,"repeat (TPR 4 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Non-catalytic subunit of the NatB complex which catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Asp-Glu. May play a role in normal cell-cycle progression. {ECO:0000269|PubMed:18570629}.; ",{"$nulls":4},"p.Ala124Asp","c.371C>A","MODERATE","124/972",4,{"$nulls":5},"5","920","593","644","429","805","505","0","0","0","0.1525",{"$nulls":20},"4.178339","1.13","1.975","1","-3.5","1.0","0.005","0.953",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","891,0","0","891","0/1","487,90","0.156","577",null,"chr12:112087714:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1585"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PBLD","chr10:68284276","PBLD(F253fs)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Phe253fs","c.755-5_767delTTTAGCTTTTCAGTGTTC","HIGH","252/288",10,{"$nulls":5},"3",null,null,"258","181","277","228",null,null,"0","0.0614",{"$nulls":5},"(PBLD|ENSG00000108187|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","369,0","0","369","0/1","270,17","0.0592","287",null,"chr10:68284276:GGAACACTGAAAAGCTAAA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0552"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PBLD","chr10:68284276","PBLD(F253fs)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Phe253fs","c.755-5_767delTTTAGCTTTTCAGTGTTC","HIGH","252/288",10,{"$nulls":5},"5","378","296","258","215","277","233","0","0","0","0.1717",{"$nulls":5},"(PBLD|ENSG00000108187|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","235,45","0.1607","280",null,"chr10:68284276:GGAACACTGAAAAGCTAAA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1116"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PFKL","chr21:44313134","PFKL(T195N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis (PubMed:22923583). Negatively regulates the phagocyte oxidative burst in response to bacterial infection by controlling cellular NADPH biosynthesis and NADPH oxidase-derived reactive oxygen species. Upon macrophage activation, drives the metabolic switch toward glycolysis, thus preventing glucose turnover that produces NADPH via pentose phosphate pathway (By similarity). {ECO:0000250|UniProtKB:P12382, ECO:0000255|HAMAP-Rule:MF_03184, ECO:0000269|PubMed:22923583}.; ",{"$nulls":4},"p.Thr195Asn","c.584C>A","MODERATE","195/780",5,{"$nulls":5},"4","693","672","483","452",null,null,"0","0",{"$nulls":22},"3.556002","-1.76","4.745","1","-4.69","1.0",null,"0.873",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","680,0","0","680","0/1","614,42","0.064","656",null,"chr21:44313134:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0531"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PLEKHO1","chr1:150159231","PLEKHO1(A313G)",null,null,"region of interest (Negative regulator of AP-1 activity )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the regulation of the actin cytoskeleton through its interactions with actin capping protein (CP). May function to target CK2 to the plasma membrane thereby serving as an adapter to facilitate the phosphorylation of CP by protein kinase 2 (CK2). Appears to target ATM to the plasma membrane. Appears to also inhibit tumor cell growth by inhibiting AKT- mediated cell-survival. Also implicated in PI3K-regulated muscle differentiation, the regulation of AP-1 activity (plasma membrane bound AP-1 regulator that translocates to the nucleus) and the promotion of apoptosis induced by tumor necrosis factor TNF. When bound to PKB, it inhibits it probably by decreasing PKB level of phosphorylation. {ECO:0000269|PubMed:14729969, ECO:0000269|PubMed:15706351, ECO:0000269|PubMed:15831458, ECO:0000269|PubMed:16325375, ECO:0000269|PubMed:16987810, ECO:0000269|PubMed:17197158, ECO:0000269|PubMed:17942896}.; ",{"$nulls":4},"p.Ala313Gly","c.938C>G","MODERATE","313/409",6,{"$nulls":5},"5","510","589","397","464","394","469","0","0","0","0.0896",{"$nulls":20},"2.573778",".;0.6",".;1.825","0.998266;0.99779;0.99779","-2.5;-1.2",".;0.877","0.038;0.023","0.546;0.413",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","497,0","0","497","0/1","537,49","0.0836","586",null,"chr1:150159231:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0884"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PLEKHO1","chr1:150159231","PLEKHO1(A313G)",null,null,"region of interest (Negative regulator of AP-1 activity )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the regulation of the actin cytoskeleton through its interactions with actin capping protein (CP). May function to target CK2 to the plasma membrane thereby serving as an adapter to facilitate the phosphorylation of CP by protein kinase 2 (CK2). Appears to target ATM to the plasma membrane. Appears to also inhibit tumor cell growth by inhibiting AKT- mediated cell-survival. Also implicated in PI3K-regulated muscle differentiation, the regulation of AP-1 activity (plasma membrane bound AP-1 regulator that translocates to the nucleus) and the promotion of apoptosis induced by tumor necrosis factor TNF. When bound to PKB, it inhibits it probably by decreasing PKB level of phosphorylation. {ECO:0000269|PubMed:14729969, ECO:0000269|PubMed:15706351, ECO:0000269|PubMed:15831458, ECO:0000269|PubMed:16325375, ECO:0000269|PubMed:16987810, ECO:0000269|PubMed:17197158, ECO:0000269|PubMed:17942896}.; ",{"$nulls":4},"p.Ala313Gly","c.938C>G","MODERATE","313/409",6,{"$nulls":5},"5","510","720","397","533","395","543","0","0","0","0.1087",{"$nulls":20},"2.573778",".;0.6",".;1.825","0.998266;0.99779;0.99779","-2.5;-1.2",".;0.877","0.038;0.023","0.546;0.413",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","497,0","0","497","0/1","631,75","0.1062","706",null,"chr1:150159231:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1088"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PLK4","chr4:127886508","PLK4(D380H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Microcephaly and chorioretinopathy, autosomal recessive, 2 (MCCRP2) [MIM:616171]: A severe disorder characterized by microcephaly, delayed psychomotor development, growth retardation with dwarfism, and ocular abnormalities. {ECO:0000269|PubMed:25344692}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine-protein kinase that plays a central role in centriole duplication. Able to trigger procentriole formation on the surface of the parental centriole cylinder, leading to the recruitment of centriole biogenesis proteins such as SASS6, CENPJ/CPAP, CCP110, CEP135 and gamma-tubulin. When overexpressed, it is able to induce centrosome amplification through the simultaneous generation of multiple procentrioles adjoining each parental centriole during S phase. Phosphorylates 'Ser-151' of FBXW5 during the G1/S transition, leading to inhibit FBXW5 ability to ubiquitinate SASS6. Its central role in centriole replication suggests a possible role in tumorigenesis, centrosome aberrations being frequently observed in tumors. Also involved in deuterosome-mediated centriole amplification in multiciliated that can generate more than 100 centrioles. Also involved in trophoblast differentiation by phosphorylating HAND1, leading to disrupt the interaction between HAND1 and MDFIC and activate HAND1. Phosphorylates CDC25C and CHEK2. Required for the recruitment of STIL to the centriole and for STIL-mediated centriole amplification (PubMed:22020124). {ECO:0000269|PubMed:16244668, ECO:0000269|PubMed:16326102, ECO:0000269|PubMed:17681131, ECO:0000269|PubMed:18239451, ECO:0000269|PubMed:19164942, ECO:0000269|PubMed:21725316, ECO:0000269|PubMed:22020124, ECO:0000269|PubMed:27796307}.; ",{"$nulls":4},"p.Asp380His","c.1138G>C","MODERATE","380/970",5,{"$nulls":5},"5","402","337","296","262","360","298","0","0","0","0.1342",{"$nulls":20},"3.884114","0.93","2.295;.;.;.;.","1","-3.25;-3.12;-3.18;-3.24;-3.18","1.0;.;1.0;.;.","0.001;0.001;0.001;0.008;0.002","0.4;0.47;0.431;0.441;0.402",{"$nulls":3},"Unknown",-1,"AR","Microcephaly and chorioretinopathy, autosomal recessive 2","Musculoskeletal; Neurologic; Ophthalmologic",{"$nulls":3},"C4015388","0/0","397,0","0","397","0/1","286,49","0.1463","335",null,"chr4:127886508:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1527"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PLK4","chr4:127886508","PLK4(D380H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Microcephaly and chorioretinopathy, autosomal recessive, 2 (MCCRP2) [MIM:616171]: A severe disorder characterized by microcephaly, delayed psychomotor development, growth retardation with dwarfism, and ocular abnormalities. {ECO:0000269|PubMed:25344692}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine-protein kinase that plays a central role in centriole duplication. Able to trigger procentriole formation on the surface of the parental centriole cylinder, leading to the recruitment of centriole biogenesis proteins such as SASS6, CENPJ/CPAP, CCP110, CEP135 and gamma-tubulin. When overexpressed, it is able to induce centrosome amplification through the simultaneous generation of multiple procentrioles adjoining each parental centriole during S phase. Phosphorylates 'Ser-151' of FBXW5 during the G1/S transition, leading to inhibit FBXW5 ability to ubiquitinate SASS6. Its central role in centriole replication suggests a possible role in tumorigenesis, centrosome aberrations being frequently observed in tumors. Also involved in deuterosome-mediated centriole amplification in multiciliated that can generate more than 100 centrioles. Also involved in trophoblast differentiation by phosphorylating HAND1, leading to disrupt the interaction between HAND1 and MDFIC and activate HAND1. Phosphorylates CDC25C and CHEK2. Required for the recruitment of STIL to the centriole and for STIL-mediated centriole amplification (PubMed:22020124). {ECO:0000269|PubMed:16244668, ECO:0000269|PubMed:16326102, ECO:0000269|PubMed:17681131, ECO:0000269|PubMed:18239451, ECO:0000269|PubMed:19164942, ECO:0000269|PubMed:21725316, ECO:0000269|PubMed:22020124, ECO:0000269|PubMed:27796307}.; ",{"$nulls":4},"p.Asp380His","c.1138G>C","MODERATE","380/970",5,{"$nulls":5},"5","402","237","296","188","362","208","0","0","0","0.1875",{"$nulls":20},"3.884114","0.93","2.295;.;.;.;.","1","-3.25;-3.12;-3.18;-3.24;-3.18","1.0;.;1.0;.;.","0.001;0.001;0.001;0.008;0.002","0.4;0.47;0.431;0.441;0.402",{"$nulls":3},"Unknown",-1,"AR","Microcephaly and chorioretinopathy, autosomal recessive 2","Musculoskeletal; Neurologic; Ophthalmologic",{"$nulls":3},"C4015388","0/0","396,0","0","396","0/1","187,49","0.2076","236",null,"chr4:127886508:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2234"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PPP1R8","chr1:27830851","PPP1R8(N6Y)",null,null,"region of interest (Interaction with CDC5L, SF3B1 and MELK ), splice variant (In isoform Gamma. ), splice variant (In isoform Beta. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibitor subunit of the major nuclear protein phosphatase-1 (PP-1). It has RNA-binding activity but does not cleave RNA and may target PP-1 to RNA-associated substrates. May also be involved in pre-mRNA splicing. Binds DNA and might act as a transcriptional repressor. Seems to be required for cell proliferation.; ",{"$nulls":4},"p.Asn6Tyr","c.16A>T","MODERATE","6/351",1,{"$nulls":5},"5","367","288","254","201","331","262","0","0","0","0.0687",{"$nulls":20},"3.369486","0.89","1.245","1;1;0.883798","-1.3","0.393","0.038","0.547",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","358,0","0","358","0/1","260,20","0.0714","280",null,"chr1:27830851:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0697"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PPP1R8","chr1:27830851","PPP1R8(N6Y)",null,null,"region of interest (Interaction with CDC5L, SF3B1 and MELK ), splice variant (In isoform Gamma. ), splice variant (In isoform Beta. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibitor subunit of the major nuclear protein phosphatase-1 (PP-1). It has RNA-binding activity but does not cleave RNA and may target PP-1 to RNA-associated substrates. May also be involved in pre-mRNA splicing. Binds DNA and might act as a transcriptional repressor. Seems to be required for cell proliferation.; ",{"$nulls":4},"p.Asn6Tyr","c.16A>T","MODERATE","6/351",1,{"$nulls":5},"5","367","301","254","206","328","277","0","0","0","0.1805",{"$nulls":20},"3.369486","0.89","1.245","1;1;0.883798","-1.3","0.393","0.038","0.547",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","358,0","0","358","0/1","241,53","0.1803","294",null,"chr1:27830851:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1796"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PRDM16","chr1:3418679","PRDM16(K958N)",null,null,"zinc finger region (C2H2-type 8 ), region of interest (Interaction with CTBP1, CTBP2 and ZNF516 ), region of interest (Mediates interaction with SKI and regulation of TGF-beta signaling )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cardiomyopathy, dilated 1LL (CMD1LL) [MIM:615373]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:23768516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving PRDM16 is found in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Reciprocal translocation t(1;3)(p36;q21). Isoform 4 is specifically expressed in adult T-cell leukemia. {ECO:0000269|PubMed:11050005, ECO:0000269|PubMed:12557231}.; ","FUNCTION: Binds DNA and functions as a transcriptional regulator. Functions in the differentiation of brown adipose tissue (BAT) which is specialized in dissipating chemical energy in the form of heat in response to cold or excess feeding while white adipose tissue (WAT) is specialized in the storage of excess energy and the control of systemic metabolism. Together with CEBPB, regulates the differentiation of myoblastic precursors into brown adipose cells. Functions also as a repressor of TGF-beta signaling. Isoform 4 may regulate granulocytes differentiation. {ECO:0000269|PubMed:12816872, ECO:0000269|PubMed:14656887, ECO:0000269|PubMed:19049980}.; ","level2",{"$nulls":3},"p.Lys958Asn","c.2874G>C","MODERATE","958/1276",12,{"$nulls":5},"3","534","483","361","314",null,null,"0.0041","0.0041",{"$nulls":22},"4.402285","-0.29",".;2.42;.;2.42;.","0.999988;0.999988;0.999988;0.999988;0.999994;0.999988;0.999988;0.999988","-4.66;-4.73;-4.66;-4.73;-4.66",".;0.837;.;0.999;.","0.0","0.728;0.714;0.73;0.72;.",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, dilated, ILL; Left ventricular noncompaction 8","Cardiovascular","COSMIC",null,null,"C3809288","0/0","458,0","0","458","0/1","375,20","0.0506","395",null,"chr1:3418679:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.051"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PRDM16","chr1:3418679","PRDM16(K958N)",null,null,"zinc finger region (C2H2-type 8 ), region of interest (Interaction with CTBP1, CTBP2 and ZNF516 ), region of interest (Mediates interaction with SKI and regulation of TGF-beta signaling )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cardiomyopathy, dilated 1LL (CMD1LL) [MIM:615373]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:23768516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving PRDM16 is found in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Reciprocal translocation t(1;3)(p36;q21). Isoform 4 is specifically expressed in adult T-cell leukemia. {ECO:0000269|PubMed:11050005, ECO:0000269|PubMed:12557231}.; ","FUNCTION: Binds DNA and functions as a transcriptional regulator. Functions in the differentiation of brown adipose tissue (BAT) which is specialized in dissipating chemical energy in the form of heat in response to cold or excess feeding while white adipose tissue (WAT) is specialized in the storage of excess energy and the control of systemic metabolism. Together with CEBPB, regulates the differentiation of myoblastic precursors into brown adipose cells. Functions also as a repressor of TGF-beta signaling. Isoform 4 may regulate granulocytes differentiation. {ECO:0000269|PubMed:12816872, ECO:0000269|PubMed:14656887, ECO:0000269|PubMed:19049980}.; ","level2",{"$nulls":3},"p.Lys958Asn","c.2874G>C","MODERATE","958/1276",12,{"$nulls":5},"3",null,null,"361","263","363","283",null,null,"0","0.159",{"$nulls":20},"4.402285","-0.29",".;2.42;.;2.42;.","0.999988;0.999988;0.999988;0.999988;0.999994;0.999988;0.999988;0.999988","-4.66;-4.73;-4.66;-4.73;-4.66",".;0.837;.;0.999;.","0.0","0.728;0.714;0.73;0.72;.",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, dilated, ILL; Left ventricular noncompaction 8","Cardiovascular","COSMIC",null,null,"C3809288","0/0","486,2","0.0041","534","0/1","308,53","0.1468","393",null,"chr1:3418679:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1635"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PRPF4B","chr6:4044021","PRPF4B(N620S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF.; ",{"$nulls":4},"p.Asn620Ser","c.1859A>G","MODERATE","620/1007",6,{"$nulls":5},"5","313","213","225","161","272","190","0","0","0","0.1421",{"$nulls":20},"2.9429119999999998","-0.19",null,"0.999822","-0.97","0.646","0.064","0.191",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","310,0","0","310","0/1","184,27","0.128","211",null,"chr6:4044021:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1491"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","PXDN","chr2:1665074","PXDN(A431G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Anterior segment dysgenesis 7 (ASGD7) [MIM:269400]: A form of anterior segment dysgenesis, a group of defects affecting anterior structures of the eye including cornea, iris, lens, trabecular meshwork, and Schlemm canal. Anterior segment dysgeneses result from abnormal migration or differentiation of the neural crest derived mesenchymal cells that give rise to components of the anterior chamber during eye development. Different anterior segment anomalies may exist alone or in combination, including iris hypoplasia, enlarged or reduced corneal diameter, corneal vascularization and opacity, posterior embryotoxon, corectopia, polycoria, abnormal iridocorneal angle, ectopia lentis, and anterior synechiae between the iris and posterior corneal surface. Clinical conditions falling within the phenotypic spectrum of anterior segment dysgeneses include aniridia, Axenfeld anomaly, Reiger anomaly/syndrome, Peters anomaly, and iridogoniodysgenesis. ASGD7 is an autosomal recessive disease. {ECO:0000269|PubMed:21907015}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Displays low peroxidase activity and is likely to participate in H(2)O(2) metabolism and peroxidative reactions in the cardiovascular system. Plays a role in extracellular matrix formation. {ECO:0000269|PubMed:18929642, ECO:0000269|PubMed:19590037}.; ",{"$nulls":4},"p.Ala431Gly","c.1292C>G","MODERATE","431/1479",11,{"$nulls":5},"5","395","320","266","210","376","299","0","0","0","0.0836",{"$nulls":20},"3.7686830000000002","1.69","1.17","0.999998","-2.25","0.63","0.109","0.601",{"$nulls":3},"Unknown",-1,"AR","Corneal opacification with other ocular anomalies","Ophthalmologic",null,"Drosophila peroxidasin is an extracellular matrix-associated peroxidase (Horikoshi et al., 1999 [PubMed 10441517]). It is expressed exclusively in hemocytes derived from head mesoderm at a very early stage of differentiation. Peroxidasin exists as a homotrimer with a unique hybrid structure that combines an enzymatically functional peroxidase domain with motifs that are typically found in extracellular matrix-associated proteins. It is a secreted protein that contains a secretory recognition sequence at its N terminus. Peroxidasin catalyzes hydrogen peroxide-driven radioiodination, oxidations, and the formation of dityrosine in vitro. It is also thought to function in extracellular matrix consolidation, phagocytosis, and defense.[supplied by OMIM, Jul 2009].  ",null,"C3151617","0/0","387,0","0","387","0/1","285,27","0.0865","312",null,"chr2:1665074:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.081"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","PXDN","chr2:1665074","PXDN(A431G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Anterior segment dysgenesis 7 (ASGD7) [MIM:269400]: A form of anterior segment dysgenesis, a group of defects affecting anterior structures of the eye including cornea, iris, lens, trabecular meshwork, and Schlemm canal. Anterior segment dysgeneses result from abnormal migration or differentiation of the neural crest derived mesenchymal cells that give rise to components of the anterior chamber during eye development. Different anterior segment anomalies may exist alone or in combination, including iris hypoplasia, enlarged or reduced corneal diameter, corneal vascularization and opacity, posterior embryotoxon, corectopia, polycoria, abnormal iridocorneal angle, ectopia lentis, and anterior synechiae between the iris and posterior corneal surface. Clinical conditions falling within the phenotypic spectrum of anterior segment dysgeneses include aniridia, Axenfeld anomaly, Reiger anomaly/syndrome, Peters anomaly, and iridogoniodysgenesis. ASGD7 is an autosomal recessive disease. {ECO:0000269|PubMed:21907015}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Displays low peroxidase activity and is likely to participate in H(2)O(2) metabolism and peroxidative reactions in the cardiovascular system. Plays a role in extracellular matrix formation. {ECO:0000269|PubMed:18929642, ECO:0000269|PubMed:19590037}.; ",{"$nulls":4},"p.Ala431Gly","c.1292C>G","MODERATE","431/1479",11,{"$nulls":5},"5","395","261","266","173","376","236","0","0","0","0.1864",{"$nulls":20},"3.7686830000000002","1.69","1.17","0.999998","-2.25","0.63","0.109","0.601",{"$nulls":3},"Unknown",-1,"AR","Corneal opacification with other ocular anomalies","Ophthalmologic",null,"Drosophila peroxidasin is an extracellular matrix-associated peroxidase (Horikoshi et al., 1999 [PubMed 10441517]). It is expressed exclusively in hemocytes derived from head mesoderm at a very early stage of differentiation. Peroxidasin exists as a homotrimer with a unique hybrid structure that combines an enzymatically functional peroxidase domain with motifs that are typically found in extracellular matrix-associated proteins. It is a secreted protein that contains a secretory recognition sequence at its N terminus. Peroxidasin catalyzes hydrogen peroxide-driven radioiodination, oxidations, and the formation of dityrosine in vitro. It is also thought to function in extracellular matrix consolidation, phagocytosis, and defense.[supplied by OMIM, Jul 2009].  ",null,"C3151617","0/0","388,0","0","388","0/1","210,48","0.186","258",null,"chr2:1665074:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2023"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","RCCD1","chr15:90957490","RCCD1(W182R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a coregulator of KDM8 to promote histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8 (PubMed:24981860). Possibly together with KDM8, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha- tubulin deacetylation and cytoskeletal microtubule stability and thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8 (PubMed:28455245). {ECO:0000269|PubMed:24981860, ECO:0000269|PubMed:28455245}.; ",{"$nulls":4},"p.Trp182Arg","c.544T>C","MODERATE","182/376",3,{"$nulls":5},"5","326","240","284","208","254","179","0","0","0","0.0726",{"$nulls":20},"4.219454","-3.05","4.385;.;4.385","0.999999","-9.98;-9.65;-9.98","0.952;0.94;0.952","0.0","0.791;0.786;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","323,0","0","323","0/1","218,16","0.0684","234",null,"chr15:90957490:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0721"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","RCCD1","chr15:90957490","RCCD1(W182R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a coregulator of KDM8 to promote histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8 (PubMed:24981860). Possibly together with KDM8, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha- tubulin deacetylation and cytoskeletal microtubule stability and thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8 (PubMed:28455245). {ECO:0000269|PubMed:24981860, ECO:0000269|PubMed:28455245}.; ",{"$nulls":4},"p.Trp182Arg","c.544T>C","MODERATE","182/376",3,{"$nulls":5},"5","326","217","284","185","252","158","0","0","0","0.1392",{"$nulls":20},"4.219454","-3.05","4.385;.;4.385","0.999999","-9.98;-9.65;-9.98","0.952;0.94;0.952","0.0","0.791;0.786;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","324,0","0","324","0/1","183,30","0.1408","213",null,"chr15:90957490:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1351"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","RCSD1","chr1:167697361","RCSD1(T246I)",null,null,"domain (RCSD ), splice variant (In isoform 2. )","modified-residue:phosphothreonine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Stress-induced phosphorylation of CAPZIP may regulate the ability of F-actin-capping protein to remodel actin filament assembly. {ECO:0000269|PubMed:15850461}.; ",{"$nulls":4},"p.Thr246Ile","c.737C>T","MODERATE","246/416",6,{"$nulls":5},"5","457","455","350","354","398","397","0","0","0","0.0705",{"$nulls":20},"0.795007","0.85;0.87",".;0.71","1","-2.06","0.021;0.012","0.13","0.114;0.069",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","452,0","0","452","0/1","415,37","0.0819","452",null,"chr1:167697361:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0763"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","RCSD1","chr1:167697361","RCSD1(T246I)",null,null,"domain (RCSD ), splice variant (In isoform 2. )","modified-residue:phosphothreonine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Stress-induced phosphorylation of CAPZIP may regulate the ability of F-actin-capping protein to remodel actin filament assembly. {ECO:0000269|PubMed:15850461}.; ",{"$nulls":4},"p.Thr246Ile","c.737C>T","MODERATE","246/416",6,{"$nulls":5},"5","457","391","350","303","395","347","0","0","0","0.1412",{"$nulls":20},"0.795007","0.85;0.87",".;0.71","1","-2.06","0.021;0.012","0.13","0.114;0.069",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","451,0","0","451","0/1","326,59","0.1532","385",null,"chr1:167697361:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.165"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SDPR","chr2:191835996","SDPR(T402R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr402Arg","c.1205C>G","MODERATE","402/425",2,{"$nulls":5},"4","796","808","626","632","622","598","0","0","0","0.112",{"$nulls":20},"1.377567","-0.13",null,"1","-0.6","0.302","0.008","0.103",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","766,0","0","766","0/1","690,79","0.1027","769",null,"chr2:191835996:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0997"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SDPR","chr2:191835996","SDPR(T402R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr402Arg","c.1205C>G","MODERATE","402/425",2,{"$nulls":5},"3","796","810","626","622",null,null,"0","0",{"$nulls":22},"1.377567","-0.13",null,"1","-0.6","0.302","0.008","0.103",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","783,1","0.0013","784","0/1","534,253","0.3215","787",null,"chr2:191835996:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3103"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SIGLEC12","chr19:51499986","SIGLEC12(F248V)",null,null,"topological domain (Extracellular ), domain (Ig-like V-type 2 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.; ",{"$nulls":4},"p.Phe248Val","c.742T>G","MODERATE","248/595",2,{"$nulls":5},"5","388","280","319","242","291","231","0","0","0","0.0693",{"$nulls":20},"2.660506","0.89","3.555;.","1","-5.95;.","1.0;0.999","0.001;.","0.448;0.505",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","377,0","0","377","0/1","257,18","0.0655","275",null,"chr19:51499986:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.062"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SIGLEC12","chr19:51499986","SIGLEC12(F248V)",null,null,"topological domain (Extracellular ), domain (Ig-like V-type 2 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.; ",{"$nulls":4},"p.Phe248Val","c.742T>G","MODERATE","248/595",2,{"$nulls":5},"5","388","264","319","221","292","222","0","0","0","0.2568",{"$nulls":20},"2.660506","0.89","3.555;.","1","-5.95;.","1.0;0.999","0.001;.","0.448;0.505",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","377,0","0","377","0/1","194,58","0.2302","252",null,"chr19:51499986:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2217"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SLC39A10","chr2:195728350","SLC39A10(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: May act as a zinc-influx transporter. {ECO:0000269|PubMed:17359283}.; ",{"$nulls":5},"c.2337+1G>T","HIGH",null,9,{"$nulls":5},"4","526","394","375","272","499","359","0","0","0","0.0864",{"$nulls":5},"(SLC39A10|ENSG00000196950|1|1.00)",{"$nulls":14},"5.992271",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","515,0","0","515","0/1","353,37","0.0949","390",null,"chr2:195728350:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0993"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SLC39A10","chr2:195728350","SLC39A10(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: May act as a zinc-influx transporter. {ECO:0000269|PubMed:17359283}.; ",{"$nulls":5},"c.2337+1G>T","HIGH",null,9,{"$nulls":5},"4","526","480","375","331","499","439","0","0","0","0.3144",{"$nulls":5},"(SLC39A10|ENSG00000196950|1|1.00)",{"$nulls":14},"5.992271",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","513,1","0.0019","514","0/1","323,149","0.3157","472",null,"chr2:195728350:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2961"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SLC9A3","chr5:524303","SLC9A3(R7L)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Diarrhea 8, secretory sodium, congenital (DIAR8) [MIM:616868]: A disease characterized by watery secretory diarrhea with prenatal onset, prominent abdominal distension after birth due to dilated fluid-filled loops of intestine, elevated fecal sodium concentrations and low urinary sodium concentrations. {ECO:0000269|PubMed:26358773}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient (PubMed:26358773). Plays an important role in signal transduction. {ECO:0000269|PubMed:26358773}.; ",{"$nulls":4},"p.Arg7Leu","c.20G>T","MODERATE","7/834",1,{"$nulls":5},"3","185","169","141","131",null,null,"0","0",{"$nulls":22},"0.224054",".;1.09;0.67",".;0.975;0.975","1",".;-0.32;-0.56",".;0.0;.",".;0.506;0.515",".;0.088;0.08",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN515063","0/0","183,0","0","183","0/1","154,16","0.0941","170",null,"chr5:524303:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0916"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SMPDL3B","chr1:27953350","SMPDL3B(K171fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Lipid-modulating phosphodiesterase (PubMed:26095358). Active on the surface of macrophages and dendritic cells and strongly influences macrophage lipid composition and membrane fluidity. Acts as a negative regulator of Toll-like receptor signaling (By similarity). {ECO:0000250|UniProtKB:P58242, ECO:0000269|PubMed:26095358}.; ",{"$nulls":4},"p.Lys171fs","c.511_517+4delAAAAAAGGTAC","HIGH","171/455",4,{"$nulls":5},"5","286","282","174","190","197","200","0","0","0","0.095",{"$nulls":5},"(SMPDL3B|ENSG00000130768|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","266,0","0","266","0/1","241,25","0.094","266",null,"chr1:27953350:TCAAAAAAGGTA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1105"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SMPDL3B","chr1:27953350","SMPDL3B(K171fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Lipid-modulating phosphodiesterase (PubMed:26095358). Active on the surface of macrophages and dendritic cells and strongly influences macrophage lipid composition and membrane fluidity. Acts as a negative regulator of Toll-like receptor signaling (By similarity). {ECO:0000250|UniProtKB:P58242, ECO:0000269|PubMed:26095358}.; ",{"$nulls":4},"p.Lys171fs","c.511_517+4delAAAAAAGGTAC","HIGH","171/455",4,{"$nulls":5},"5","286","242","174","167","197","171","0","0","0","0.2047",{"$nulls":5},"(SMPDL3B|ENSG00000130768|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","266,0","0","266","0/1","179,38","0.1751","217",null,"chr1:27953350:TCAAAAAAGGTA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1976"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SPPL3","chr12:120782708","SPPL3(S150F)",null,null,"transmembrane region (Helical ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Intramembrane-cleaving aspartic protease (I-CLiP) that cleaves type II membrane protein substrates in or close to their luminal transmembrane domain boundaries (PubMed:16873890, PubMed:25354954, PubMed:25827571). Acts like a sheddase by mediating the proteolytic release and secretion of active site- containing ectodomains of glycan-modifiying glycosidase and glycosyltransferase enzymes such as MGAT5, B4GAT1 and B4GALT1 (PubMed:25354954, PubMed:25827571). Catalyzes the intramembrane cleavage of the envelope glycoprotein gp130 and/or the leader peptide gp18LP of the simian foamy virus independent of prior ectodomain shedding by furin or furin-like proprotein convertase (PC)-mediated cleavage proteolysis (PubMed:23132852). May also have the ability to serve as a shedding protease for subsequent intramembrane proteolysis by SPPL2A and SPPL2B of the envelope glycoprotein gp130 (PubMed:23132852). Plays a role in the regulation of cellular glycosylation processes (PubMed:25354954). Required to link T-cell antigen receptor (TCR) and calcineurin- NFAT signaling cascades in lymphocytes by promoting the association of STIM1 and ORAI1 during store-operated calcium entry (SOCE) in a protease-independent manner (PubMed:25384971). {ECO:0000269|PubMed:16873890, ECO:0000269|PubMed:23132852, ECO:0000269|PubMed:25354954, ECO:0000269|PubMed:25384971, ECO:0000269|PubMed:25827571}.; ",{"$nulls":4},"p.Ser150Phe","c.449C>T","MODERATE","150/384",6,{"$nulls":5},"5","103","122","74","84","94","104","0","0","0","0.1154",{"$nulls":20},"4.21282","1.91",null,"1","-3.51;-3.43;-3.29;-3.62;-4.46",null,"0.012;0.009;0.01;0.016;0.001","0.787;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","103,0","0","103","0/1","106,14","0.1167","120",null,"chr12:120782708:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.131"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SPPL3","chr12:120782708","SPPL3(S150F)",null,null,"transmembrane region (Helical ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Intramembrane-cleaving aspartic protease (I-CLiP) that cleaves type II membrane protein substrates in or close to their luminal transmembrane domain boundaries (PubMed:16873890, PubMed:25354954, PubMed:25827571). Acts like a sheddase by mediating the proteolytic release and secretion of active site- containing ectodomains of glycan-modifiying glycosidase and glycosyltransferase enzymes such as MGAT5, B4GAT1 and B4GALT1 (PubMed:25354954, PubMed:25827571). Catalyzes the intramembrane cleavage of the envelope glycoprotein gp130 and/or the leader peptide gp18LP of the simian foamy virus independent of prior ectodomain shedding by furin or furin-like proprotein convertase (PC)-mediated cleavage proteolysis (PubMed:23132852). May also have the ability to serve as a shedding protease for subsequent intramembrane proteolysis by SPPL2A and SPPL2B of the envelope glycoprotein gp130 (PubMed:23132852). Plays a role in the regulation of cellular glycosylation processes (PubMed:25354954). Required to link T-cell antigen receptor (TCR) and calcineurin- NFAT signaling cascades in lymphocytes by promoting the association of STIM1 and ORAI1 during store-operated calcium entry (SOCE) in a protease-independent manner (PubMed:25384971). {ECO:0000269|PubMed:16873890, ECO:0000269|PubMed:23132852, ECO:0000269|PubMed:25354954, ECO:0000269|PubMed:25384971, ECO:0000269|PubMed:25827571}.; ",{"$nulls":4},"p.Ser150Phe","c.449C>T","MODERATE","150/384",6,{"$nulls":5},"5","103","85","74","53","95","77","0","0","0","0.3506",{"$nulls":20},"4.21282","1.91",null,"1","-3.51;-3.43;-3.29;-3.62;-4.46",null,"0.012;0.009;0.01;0.016;0.001","0.787;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","103,0","0","103","0/1","52,31","0.3735","83",null,"chr12:120782708:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3774"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SULT2B1","chr19:48587313","SULT2B1(R100Q)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs138292714",2.3255813953488373E-4,null,"FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol. Plays a role in epidermal cholesterol metabolism and in the regulation of epidermal proliferation and differentiation (PubMed:28575648). {ECO:0000269|PubMed:12145317, ECO:0000269|PubMed:28575648, ECO:0000269|PubMed:9799594}.; ",{"$nulls":5},"c.299G>A","HIGH",null,3,1,{"$nulls":4},"4","779","499","558","353","731","450","0.0013","0.0013","0","0.0778",{"$nulls":20},"4.197237","-1.75","2.535;.","0.70735;0.667181","-3.9","1.0","0.01;0.011","0.7",{"$nulls":3},"ESP6500_EA_AF",2.3255813953488373E-4,{"$nulls":6},"C4539754","0/0","766,1","0.0013","767","0/1","454,40","0.081","494",null,"chr19:48587313:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0793"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SULT2B1","chr19:48587313","SULT2B1(R100Q)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs138292714",2.3255813953488373E-4,null,"FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol. Plays a role in epidermal cholesterol metabolism and in the regulation of epidermal proliferation and differentiation (PubMed:28575648). {ECO:0000269|PubMed:12145317, ECO:0000269|PubMed:28575648, ECO:0000269|PubMed:9799594}.; ",{"$nulls":5},"c.299G>A","HIGH",null,3,1,{"$nulls":4},"4","779","519","558","360","732","486","0.0013","0.0013","0","0.2387",{"$nulls":20},"4.197237","-1.75","2.535;.","0.70735;0.667181","-3.9","1.0","0.01;0.011","0.7",{"$nulls":3},"ESP6500_EA_AF",2.3255813953488373E-4,{"$nulls":6},"C4539754","0/0","753,1","0.0013","754","0/1","381,122","0.2425","503",null,"chr19:48587313:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.225"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","SYT7","chr11:61533120","SYT7(P357A)",null,null,"topological domain (Cytoplasmic ), domain (C2 2 ), metal ion-binding site (Calcium 4), metal ion-binding site (Calcium 5)",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Ca(2+) sensor involved in Ca(2+)-dependent exocytosis of secretory and synaptic vesicles through Ca(2+) and phospholipid binding to the C2 domain (By similarity). Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity). SYT7 binds Ca(2+) with high affinity and slow kinetics compared to other synaptotagmins (By similarity). Involved in Ca(2+)-triggered lysosomal exocytosis, a major component of the plasma membrane repair (PubMed:11342594). Ca(2+)- regulated delivery of lysosomal membranes to the cell surface is also involved in the phagocytic uptake of particles by macrophages (By similarity). Ca(2+)-triggered lysosomal exocytosis also plays a role in bone remodeling by regulating secretory pathways in osteoclasts and osteoblasts (By similarity). In case of infection, involved in participates cell invasion by Trypanosoma cruzi via Ca(2+)-triggered lysosomal exocytosis (PubMed:11342594, PubMed:15811535). Involved in cholesterol transport from lysosome to peroxisome by promoting membrane contacts between lysosomes and peroxisomes: probably acts by promoting vesicle fusion by binding phosphatidylinositol-4,5-bisphosphate on peroxisomal membranes (By similarity). Acts as a key mediator of synaptic facilitation, a process also named short-term synaptic potentiation: synaptic facilitation takes place at synapses with a low initial release probability and is caused by influx of Ca(2+) into the axon terminal after spike generation, increasing the release probability of neurotransmitters (By similarity). Probably mediates synaptic facilitation by directly increasing the probability of release (By similarity). May also contribute to synaptic facilitation by regulating synaptic vesicle replenishment, a process required to ensure that synaptic vesicles are ready for the arrival of the next action potential: SYT7 is required for synaptic vesicle replenishment by acting as a sensor for Ca(2+) and by forming a complex with calmodulin (By similarity). Also acts as a regulator of Ca(2+)-dependent insulin and glucagon secretion in beta-cells (By similarity). Triggers exocytosis by promoting fusion pore opening and fusion pore expansion in chromaffin cells (By similarity). Also regulates the secretion of some non-synaptic secretory granules of specialized cells (By similarity). {ECO:0000250|UniProtKB:Q62747, ECO:0000250|UniProtKB:Q9R0N7, ECO:0000269|PubMed:11342594, ECO:0000269|PubMed:15811535}.; ",{"$nulls":4},"p.Pro357Ala","c.1069C>G","MODERATE","357/686",8,{"$nulls":5},"5","308","298","225","209","283","274","0","0","0","0.1496",{"$nulls":20},"3.083843","0.6;0.58;0.62;0.6;0.51;0.59;1.93","0.69;.;.;.;.;.;.","0.965337;0.992072;0.999932;0.997832;0.999932;0.97602","-1.71;-1.75;-1.86;-1.65;-1.86;-1.75;-1.75","0.787;.;.;.;.;.;.","0.05;0.004;0.011;0.0;0.018;0.009;0.135","0.426;0.472;0.512;0.48;0.481;0.449;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. A similar protein in rodents mediates hormone secretion and lysosome exocytosis. In humans, expression of this gene has been associated with prostate cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011].",null,null,"0/0","307,0","0","307","0/1","248,52","0.1733","300",null,"chr11:61533120:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.177"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","SYT7","chr11:61533120","SYT7(P357A)",null,null,"topological domain (Cytoplasmic ), domain (C2 2 ), metal ion-binding site (Calcium 4), metal ion-binding site (Calcium 5)",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Ca(2+) sensor involved in Ca(2+)-dependent exocytosis of secretory and synaptic vesicles through Ca(2+) and phospholipid binding to the C2 domain (By similarity). Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity). SYT7 binds Ca(2+) with high affinity and slow kinetics compared to other synaptotagmins (By similarity). Involved in Ca(2+)-triggered lysosomal exocytosis, a major component of the plasma membrane repair (PubMed:11342594). Ca(2+)- regulated delivery of lysosomal membranes to the cell surface is also involved in the phagocytic uptake of particles by macrophages (By similarity). Ca(2+)-triggered lysosomal exocytosis also plays a role in bone remodeling by regulating secretory pathways in osteoclasts and osteoblasts (By similarity). In case of infection, involved in participates cell invasion by Trypanosoma cruzi via Ca(2+)-triggered lysosomal exocytosis (PubMed:11342594, PubMed:15811535). Involved in cholesterol transport from lysosome to peroxisome by promoting membrane contacts between lysosomes and peroxisomes: probably acts by promoting vesicle fusion by binding phosphatidylinositol-4,5-bisphosphate on peroxisomal membranes (By similarity). Acts as a key mediator of synaptic facilitation, a process also named short-term synaptic potentiation: synaptic facilitation takes place at synapses with a low initial release probability and is caused by influx of Ca(2+) into the axon terminal after spike generation, increasing the release probability of neurotransmitters (By similarity). Probably mediates synaptic facilitation by directly increasing the probability of release (By similarity). May also contribute to synaptic facilitation by regulating synaptic vesicle replenishment, a process required to ensure that synaptic vesicles are ready for the arrival of the next action potential: SYT7 is required for synaptic vesicle replenishment by acting as a sensor for Ca(2+) and by forming a complex with calmodulin (By similarity). Also acts as a regulator of Ca(2+)-dependent insulin and glucagon secretion in beta-cells (By similarity). Triggers exocytosis by promoting fusion pore opening and fusion pore expansion in chromaffin cells (By similarity). Also regulates the secretion of some non-synaptic secretory granules of specialized cells (By similarity). {ECO:0000250|UniProtKB:Q62747, ECO:0000250|UniProtKB:Q9R0N7, ECO:0000269|PubMed:11342594, ECO:0000269|PubMed:15811535}.; ",{"$nulls":4},"p.Pro357Ala","c.1069C>G","MODERATE","357/686",8,{"$nulls":5},"5","308","306","225","225","283","282","0","0","0","0.3511",{"$nulls":20},"3.083843","0.6;0.58;0.62;0.6;0.51;0.59;1.93","0.69;.;.;.;.;.;.","0.965337;0.992072;0.999932;0.997832;0.999932;0.97602","-1.71;-1.75;-1.86;-1.65;-1.86;-1.75;-1.75","0.787;.;.;.;.;.;.","0.05;0.004;0.011;0.0;0.018;0.009;0.135","0.426;0.472;0.512;0.48;0.481;0.449;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. A similar protein in rodents mediates hormone secretion and lysosome exocytosis. In humans, expression of this gene has been associated with prostate cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011].",null,null,"0/0","308,0","0","308","0/1","197,110","0.3583","307",null,"chr11:61533120:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3511"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","TMEM132C","chr12:128696077","TMEM132C(R635*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1376966220",-1,{"$nulls":6},"p.Arg635*","c.1903C>T","HIGH","635/1108",7,{"$nulls":5},"4","934","669","681","493","864","620","0","0","0","0.15",{"$nulls":5},"(TMEM132C|ENSG00000181234|1|1.00)","(TMEM132C|ENSG00000181234|1|1.00)",{"$nulls":13},"7.113607",null,null,"1",{"$nulls":3},"0.289",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","905,0","0","905","0/1","547,101","0.1559","648",null,"chr12:128696077:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.144"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","TMEM132C","chr12:128696077","TMEM132C(R635*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1376966220",-1,{"$nulls":6},"p.Arg635*","c.1903C>T","HIGH","635/1108",7,{"$nulls":5},"4","934","684","681","509","863","613","0","0","0","0.2626",{"$nulls":5},"(TMEM132C|ENSG00000181234|1|1.00)","(TMEM132C|ENSG00000181234|1|1.00)",{"$nulls":13},"7.113607",null,null,"1",{"$nulls":3},"0.289",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","914,0","0","914","0/1","475,182","0.277","657",null,"chr12:128696077:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2908"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","TMEM63B","chr6:44153766","TMEM63B(S678L)",null,null,"transmembrane region (Helical ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as an osmosensitive calcium-permeable cation channel. {ECO:0000250}.; ",{"$nulls":4},"p.Ser678Leu","c.2033C>T","MODERATE","678/832",21,{"$nulls":5},"4","438","427","295","299",null,null,"0.0023","0.0023",{"$nulls":22},"2.284655","2.12","1.455","0.995683","0.46","0.001","0.705","0.746;0.747",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","433,1","0.0023","434","0/1","362,59","0.1401","421",null,"chr6:44153766:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1472"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","TMEM63C","chr14:77225459","TMEM63C(M116I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as an osmosensitive calcium-permeable cation channel. {ECO:0000269|PubMed:24503647}.; ",{"$nulls":4},"p.Met116Ile","c.348G>C","MODERATE","116/806",6,{"$nulls":5},"5","410","397","289","282","338","327","0","0","0","0.052",{"$nulls":20},"2.555996","1.24",".;1.56","0.999889","-1.37;-0.95",".;0.041","0.52;0.796",".;0.589",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","382,0","0","382","0/1","347,22","0.0596","369",null,"chr14:77225459:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0567"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","TMEM63C","chr14:77225459","TMEM63C(M116I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as an osmosensitive calcium-permeable cation channel. {ECO:0000269|PubMed:24503647}.; ",{"$nulls":4},"p.Met116Ile","c.348G>C","MODERATE","116/806",6,{"$nulls":5},"5","410","335","289","255","341","281","0","0","0","0.1886",{"$nulls":20},"2.555996","1.24",".;1.56","0.999889","-1.37;-0.95",".;0.041","0.52;0.796",".;0.589",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","379,0","0","379","0/1","261,59","0.1844","320",null,"chr14:77225459:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1765"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","TP53","chr17:7674903","TP53(R170fs)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In a sporadic cancer; somatic mutation. ), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780729. TP53(T170A)), sequence variant (In a sporadic cancer; somatic mutation. TP53(T170K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs779000871. TP53(T170M)), sequence variant (In a sporadic cancer; somatic mutation. TP53(T170P)), sequence variant (In sporadic cancers; somatic mutation. TP53(T170S))",{"$nulls":3},255,"PASS","Loss Of Function","rs1057517840",-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg170fs","c.509_510delGA","HIGH","170/410",6,{"$nulls":5},"4",null,null,"274","193","279","193",null,null,"0","0.0829",{"$nulls":5},"(TP53|ENSG00000141510|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","311,0","0","311","0/1","207,17","0.0759","224",null,"chr17:7674903:TTC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0725"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","TP53","chr17:7674903","TP53(R170fs)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In a sporadic cancer; somatic mutation. ), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780729. TP53(T170A)), sequence variant (In a sporadic cancer; somatic mutation. TP53(T170K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs779000871. TP53(T170M)), sequence variant (In a sporadic cancer; somatic mutation. TP53(T170P)), sequence variant (In sporadic cancers; somatic mutation. TP53(T170S))",{"$nulls":3},255,"PASS","Loss Of Function","rs1057517840",-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg170fs","c.509_510delGA","HIGH","170/410",6,{"$nulls":5},"5","318","222","274","189","280","194","0","0","0","0.2371",{"$nulls":5},"(TP53|ENSG00000141510|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","311,0","0","311","0/1","168,53","0.2398","221",null,"chr17:7674903:TTC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2116"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","TRIM8","chr10:102655179","TRIM8(Q258_A269del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which plays different roles in immune pathways. Participates in the activation of interferon- gamma signaling by promoting proteasomal degradation of the repressor SOCS1 (PubMed:12163497). Plays a positive role in the TNFalpha and IL-1beta signaling pathways. Mechanistically, induces the 'lys-63' polyubiquitination of MAP3K7/TAK1 component leading to the activation of NF-kappa-B (PubMed:22084099, PubMed:23152791). Modulates also STAT3 activity through negative regulation of PIAS3, either by degradation of PIAS3 through the ubiquitin-proteasome pathway or exclusion of PIAS3 from the nucleus (PubMed:20516148). {ECO:0000269|PubMed:12163497, ECO:0000269|PubMed:20516148, ECO:0000269|PubMed:22084099, ECO:0000269|PubMed:23152791}.; ",{"$nulls":4},"p.Gln258_Ala269del","c.771_806delCCAGGCCAAGTTCTGCAGCGAGAACGCAGCGCAGGC","MODERATE","257/551",3,{"$nulls":5},"4","846","486","626","365","679","429","0","0","0","0.2005",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","1046,0","0","1046","0/1","468,98","0.1731","566",null,"chr10:102655179:AAGGCCCAGGCCAAGTTCTGCAGCGAGAACGCAGCGC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1836"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","TTLL11","chr9:122093202","TTLL11(G73R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Polyglutamase which preferentially modifies alpha- tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation step (By similarity). Required for CCSAP localization to both spindle and cilia microtubules (PubMed:22493317). Generates long side-chains (By similarity). {ECO:0000250|UniProtKB:A4Q9F4, ECO:0000269|PubMed:22493317}.; ",{"$nulls":4},"p.Gly73Arg","c.217G>C","MODERATE","73/800",1,{"$nulls":5},"5","324","316","293","280","210","222","0","0","0","0.1036",{"$nulls":20},"1.528009","2.74;2.52","0.345","0.998958","-0.13;0.02","0.032;.","0.0","0.124;0.145",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","320,0","0","320","0/1","282,28","0.0903","310",null,"chr9:122093202:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0964"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","TTLL11","chr9:122093202","TTLL11(G73R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Polyglutamase which preferentially modifies alpha- tubulin. Involved in the side-chain elongation step of the polyglutamylation reaction rather than in the initiation step (By similarity). Required for CCSAP localization to both spindle and cilia microtubules (PubMed:22493317). Generates long side-chains (By similarity). {ECO:0000250|UniProtKB:A4Q9F4, ECO:0000269|PubMed:22493317}.; ",{"$nulls":4},"p.Gly73Arg","c.217G>C","MODERATE","73/800",1,{"$nulls":5},"5","324","367","293","323","210","255","0","0","0","0.2196",{"$nulls":20},"1.528009","2.74;2.52","0.345","0.998958","-0.13;0.02","0.032;.","0.0","0.124;0.145",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","320,0","0","320","0/1","293,68","0.1884","361",null,"chr9:122093202:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1858"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","UBA1","chrX:47202997","UBA1(E430Q)",null,null,"region of interest (2 approximate repeats ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Spinal muscular atrophy X-linked 2 (SMAX2) [MIM:301830]: A lethal infantile form of spinal muscular atrophy, a neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. Clinical features include hypotonia, areflexia, and multiple congenital contractures. {ECO:0000269|PubMed:18179898, ECO:0000269|PubMed:23518311}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation through the ubiquitin- proteasome system (PubMed:1606621, PubMed:1447181). Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP (PubMed:1447181). Essential for the formation of radiation- induced foci, timely DNA repair and for response to replication stress. Promotes the recruitment of TP53BP1 and BRCA1 at DNA damage sites (PubMed:22456334). {ECO:0000269|PubMed:1447181, ECO:0000269|PubMed:1606621, ECO:0000269|PubMed:22456334}.; ",{"$nulls":4},"p.Glu430Gln","c.1288G>C","MODERATE","430/1058",12,{"$nulls":5},"4","606","555","462","428","523","486","0","0","0","0.0802",{"$nulls":20},"3.90042","1.94","3.805","1","-2.94","1.0","0.0","0.825;0.826",{"$nulls":3},"Unknown",-1,"XL","Spinal muscular atrophy, X-linked 2, infantile","Musculoskeletal; Neurologic",{"$nulls":3},"C1844934","0/0","598,0","0","598","0/1","506,45","0.0817","551",null,"chrX:47202997:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0888"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","UBA1","chrX:47202997","UBA1(E430Q)",null,null,"region of interest (2 approximate repeats ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Spinal muscular atrophy X-linked 2 (SMAX2) [MIM:301830]: A lethal infantile form of spinal muscular atrophy, a neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. Clinical features include hypotonia, areflexia, and multiple congenital contractures. {ECO:0000269|PubMed:18179898, ECO:0000269|PubMed:23518311}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation through the ubiquitin- proteasome system (PubMed:1606621, PubMed:1447181). Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding a ubiquitin-E1 thioester and free AMP (PubMed:1447181). Essential for the formation of radiation- induced foci, timely DNA repair and for response to replication stress. Promotes the recruitment of TP53BP1 and BRCA1 at DNA damage sites (PubMed:22456334). {ECO:0000269|PubMed:1447181, ECO:0000269|PubMed:1606621, ECO:0000269|PubMed:22456334}.; ",{"$nulls":4},"p.Glu430Gln","c.1288G>C","MODERATE","430/1058",12,{"$nulls":5},"4","606","527","462","391","524","465","0","0","0","0.2086",{"$nulls":20},"3.90042","1.94","3.805","1","-2.94","1.0","0.0","0.825;0.826",{"$nulls":3},"Unknown",-1,"XL","Spinal muscular atrophy, X-linked 2, infantile","Musculoskeletal; Neurologic",{"$nulls":3},"C1844934","0/0","598,0","0","598","0/1","408,110","0.2124","518",null,"chrX:47202997:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2072"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","UPF2","chr10:12014177","UPF2(L385V)",null,null,"domain (MIF4G 1 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC). Recruited by UPF3B associated with the EJC core at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2-UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF3B stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA. {ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:16209946, ECO:0000269|PubMed:18066079}.; ",{"$nulls":4},"p.Leu385Val","c.1153C>G","MODERATE","385/1272",3,{"$nulls":5},"5","270","364","182","257","245","332","0","0","0","0.1024",{"$nulls":20},"3.837411","0.81","1.92","1","-2.22","0.978","0.006","0.648;0.659;0.651",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","267,0","0","267","0/1","325,37","0.1022","362",null,"chr10:12014177:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1128"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","WDR93","chr15:89701807","WDR93(G21R)",{"$nulls":6},255,"PASS","Missense","rs890887866",-1,{"$nulls":6},"p.Gly21Arg","c.61G>A","MODERATE","21/686",2,{"$nulls":5},"5","282","229","243","199","212","185","0","0","0","0.0919",{"$nulls":20},"1.7380550000000001","1.61;1.64;0.59","1.975;1.975;.","0.999995","-3.59;-3.59;-4.59","0.707;0.707;0.18","0.023;0.03;0.017","0.302;0.372;0.246",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","273,0","0","273","0/1","208,19","0.0837","227",null,"chr15:89701807:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0854"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","WDR93","chr15:89701807","WDR93(G21R)",{"$nulls":6},255,"PASS","Missense","rs890887866",-1,{"$nulls":6},"p.Gly21Arg","c.61G>A","MODERATE","21/686",2,{"$nulls":5},"5","282","241","243","201","211","191","0","0","0","0.1885",{"$nulls":20},"1.7380550000000001","1.61;1.64;0.59","1.975;1.975;.","0.999995","-3.59;-3.59;-4.59","0.707;0.707;0.18","0.023;0.03;0.017","0.302;0.372;0.246",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","273,0","0","273","0/1","193,42","0.1787","235",null,"chr15:89701807:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.194"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","WNK2","chr9:93253063","WNK2(Q673fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Serine/threonine kinase which plays an important role in the regulation of electrolyte homeostasis, cell signaling, survival, and proliferation. Acts as an activator and inhibitor of sodium-coupled chloride cotransporters and potassium-coupled chloride cotransporters respectively. Activates SLC12A2, SCNN1A, SCNN1B, SCNN1D and SGK1 and inhibits SLC12A5. Negatively regulates the EGF-induced activation of the ERK/MAPK-pathway and the downstream cell cycle progression. Affects MAPK3/MAPK1 activity by modulating the activity of MAP2K1 and this modulation depends on phosphorylation of MAP2K1 by PAK1. WNK2 acts by interfering with the activity of PAK1 by controlling the balance of the activity of upstream regulators of PAK1 activity, RHOA and RAC1, which display reciprocal activity. {ECO:0000269|PubMed:17667937, ECO:0000269|PubMed:18593598, ECO:0000269|PubMed:21733846}.; ",{"$nulls":4},"p.Gln673fs","c.2015_2026del<DELETE_NUC>insA","HIGH","673/2297",8,{"$nulls":20},"93253207",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr9:93253063:<DELETE_NUC>:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ZCCHC5","chrX:78657978","ZCCHC5(T148I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr148Ile","c.443C>T","MODERATE","148/475",2,{"$nulls":5},"5","557","441","389","324","467","370","0","0","0","0.0811",{"$nulls":20},"0.68556","2.17",null,"1","-1.0","0.139","0.003","0.02",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","548,0","0","548","0/1","404,33","0.0755","437",null,"chrX:78657978:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0802"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ZCCHC5","chrX:78657978","ZCCHC5(T148I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr148Ile","c.443C>T","MODERATE","148/475",2,{"$nulls":5},"5","557","400","389","287","465","309","0","0","0","0.1521",{"$nulls":20},"0.68556","2.17",null,"1","-1.0","0.139","0.003","0.02",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","538,0","0","538","0/1","317,65","0.1702","382",null,"chrX:78657978:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1707"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ZFP57","chr6:29672713","ZFP57(D466E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Transient neonatal diabetes mellitus 1 (TNDM1) [MIM:601410]: Neonatal diabetes is a form of diabetes mellitus defined by the onset of mild-to-severe hyperglycemia within the first months of life. In about half of the neonates, diabetes is transient and resolves at a median age of 3 months, whereas the rest have a permanent form of diabetes. {ECO:0000269|PubMed:18622393}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds to a 5'-TGCCGC-3' consensus sequence and recognizes the methylated CpG within this element (By similarity). Transcription regulator required to maintain maternal and paternal gene imprinting, a process by which gene expression is restricted in a parent of origin-specific manner by epigenetic modification of genomic DNA and chromatin, including DNA methylation. Acts by controlling DNA methylation during the earliest multicellular stages of development at multiple imprinting control regions. Required for the establishment of maternal methylation imprints at SNRPN locus. Acts as a transcriptional repressor in Schwann cells. {ECO:0000250, ECO:0000269|PubMed:18622393}.; ",{"$nulls":4},"p.Asp466Glu","c.1398C>A","MODERATE","466/536",4,{"$nulls":5},"5","651","521","510","397","499","383","0.0015","0.0015","0","0.1253",{"$nulls":20},"-0.829991","3.55;3.78;.",null,"1","0.88;0.89;.","0.0;0.0;.","1.0;1.0;.","0.041;0.041;0.024",{"$nulls":3},"Unknown",-1,"AD","Diabetes mellitus, transient neonatal, 1","Endocrine",{"$nulls":3},"C1832386","0/0","638,1","0.0016","639","0/1","440,58","0.1165","498",null,"chr6:29672713:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1159"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ZFP57","chr6:29672713","ZFP57(D466E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Transient neonatal diabetes mellitus 1 (TNDM1) [MIM:601410]: Neonatal diabetes is a form of diabetes mellitus defined by the onset of mild-to-severe hyperglycemia within the first months of life. In about half of the neonates, diabetes is transient and resolves at a median age of 3 months, whereas the rest have a permanent form of diabetes. {ECO:0000269|PubMed:18622393}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds to a 5'-TGCCGC-3' consensus sequence and recognizes the methylated CpG within this element (By similarity). Transcription regulator required to maintain maternal and paternal gene imprinting, a process by which gene expression is restricted in a parent of origin-specific manner by epigenetic modification of genomic DNA and chromatin, including DNA methylation. Acts by controlling DNA methylation during the earliest multicellular stages of development at multiple imprinting control regions. Required for the establishment of maternal methylation imprints at SNRPN locus. Acts as a transcriptional repressor in Schwann cells. {ECO:0000250, ECO:0000269|PubMed:18622393}.; ",{"$nulls":4},"p.Asp466Glu","c.1398C>A","MODERATE","466/536",4,{"$nulls":5},"5","651","541","510","429","501","423","0.0015","0.0015","0","0.4113",{"$nulls":20},"-0.829991","3.55;3.78;.",null,"1","0.88;0.89;.","0.0;0.0;.","1.0;1.0;.","0.041;0.041;0.024",{"$nulls":3},"Unknown",-1,"AD","Diabetes mellitus, transient neonatal, 1","Endocrine",{"$nulls":3},"C1832386","0/0","642,1","0.0016","643","0/1","314,216","0.4075","530",null,"chr6:29672713:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4009"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ZFYVE1","chr14:72998063","ZFYVE1(L246V)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu246Val","c.736C>G","MODERATE","246/789",3,1,{"$nulls":4},"5","1046","693","734","509","931","610","0","0","0","0.1557",{"$nulls":20},"1.824791","0.05",".;0;0","0.96859","0.25","0.523;.;0.41","0.064;0.089;0.073","0.182;0.049;0.045",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1025,0","0","1025","0/1","557,112","0.1674","669",null,"chr14:72998063:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.167"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ZNF3","chr7:100075188","ZNF3(R73T)",null,null,"domain (KRAB )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in cell differentiation and/or proliferation.; ",{"$nulls":4},"p.Arg73Thr","c.218G>C","MODERATE","73/446",5,{"$nulls":5},"4","516","443","383","327","440","383","0","0","0","0.1645",{"$nulls":20},"3.505616","4.08","3.955;3.955;3.955;3.955;.;.;.;.;.","0.587563","-5.37;-4.55;-4.55;-4.55;-5.74;-5.51;-5.51;-5.59;-5.28","1.0;0.999;0.999;0.999;.;.;.;.;.","0.001;0.002;0.002;0.002;0.004;0.0;0.0;0.002;0.002","0.707;0.694;0.698;0.696;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","498,0","0","498","0/1","359,75","0.1728","434",null,"chr7:100075188:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1713"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ZNF814","chr19:57872940","ZNF814(S803_T816del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Ser803_Thr816del","c.2408_2449delGTGAATGTGGAAAATCTTTTGCTGAAAGCTCCAGTCTCACTA","MODERATE","803/855",3,{"$nulls":5},"4","326","263","269","209","164","135","0","0","0","0.1704",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","475,0","0","475","0/1","326,47","0.126","373",null,"chr19:57872940:TTAGTGAGACTGGAGCTTTCAGCAAAAGATTTTCCACATTCAC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1579"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ZNF814","chr19:57872940","ZNF814(S803_T816del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Ser803_Thr816del","c.2408_2449delGTGAATGTGGAAAATCTTTTGCTGAAAGCTCCAGTCTCACTA","MODERATE","803/855",3,{"$nulls":5},"4","326","287","269","250","164","126","0","0","0","0.1984",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","475,0","0","475","0/1","320,68","0.1753","388",null,"chr19:57872940:TTAGTGAGACTGGAGCTTTCAGCAAAAGATTTTCCACATTCAC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.208"]
["05PG","T10","JLPIKTOR_JLPIKTOR_17113005PG","ZNF92","chr7:65399511","ZNF92(S466L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ser466Leu","c.1397C>T","MODERATE","466/586",4,{"$nulls":5},"5","208","198","167","166","110","124","0","0","0","0.0565",{"$nulls":20},"1.415716","3.19","2.11;.;.;.","1","-5.33","0.338;0.688;.;.","0.018;0.011;0.009;0.009","0.2;0.246;0.166;0.174",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","206,0","0","206","0/1","184,17","0.0846","201",null,"chr7:65399511:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0964"]
["05PG","T11","JLPIKTOR_JLPIKTOR_17113005PG","ZNF92","chr7:65399511","ZNF92(S466L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ser466Leu","c.1397C>T","MODERATE","466/586",4,{"$nulls":5},"5","208","161","167","127","110","96","0","0","0","0.1875",{"$nulls":20},"1.415716","3.19","2.11;.;.;.","1","-5.33","0.338;0.688;.;.","0.018;0.011;0.009;0.009","0.2;0.246;0.166;0.174",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","206,0","0","206","0/1","124,33","0.2102","157",null,"chr7:65399511:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113005PG","somatic","somatic","JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113005PG/somatic/JLPIKTOR_17113005PG_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113005PG_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2205"]

{"sheet":"06BH","index":4,"n_rows":256,"n_cols":107,"rows_kept":256}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","AADACL4","chr1:12666163","AADACL4(Q218*)",{"$nulls":6},255,"PASS","Loss Of Function","rs138451476",1.1627906976744188E-4,{"$nulls":6},"p.Gln218*","c.652C>T","HIGH","218/407",4,{"$nulls":5},"5","1027","688","813","528","868","569","0","0","0","0.1019",{"$nulls":20},"7.029232",null,null,"1",{"$nulls":3},"0.131",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,{"$nulls":7},"0/0","994,0","0","994","0/1","602,67","0.1001","669",null,"chr1:12666163:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0985"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","AADACL4","chr1:12666163","AADACL4(Q218*)",{"$nulls":6},255,"PASS","Loss Of Function","rs138451476",1.1627906976744188E-4,{"$nulls":6},"p.Gln218*","c.652C>T","HIGH","218/407",4,{"$nulls":5},"5","1027","553","813","420","868","447","0","0","0","0.349",{"$nulls":20},"7.029232",null,null,"1",{"$nulls":3},"0.131",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,{"$nulls":7},"0/0","993,0","0","993","0/1","356,179","0.3346","535",null,"chr1:12666163:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3214"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ABHD17B","chr9:71866951","ABHD17B(D235N)",null,null,"active site (Charge relay system )","active-site:Charge_relay_system","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Hydrolyzes fatty acids from S-acylated cysteine residues in proteins (PubMed:26701913). Has depalmitoylating activity towards DLG4/PSD95 (PubMed:26701913). Has depalmitoylating activity towards GAP43 (By similarity). Has depalmitoylating activity towards MAP6 (By similarity). Has depalmitoylating activity towards NRAS (PubMed:26701913). {ECO:0000250|UniProtKB:Q7M759, ECO:0000269|PubMed:26701913}.; ",{"$nulls":4},"p.Asp235Asn","c.703G>A","MODERATE","235/293",4,{"$nulls":5},"4","479","328","319","221",null,null,"0","0",{"$nulls":22},"4.105014","-1.99","4.905","1","-4.33","1.0","0.0","0.918;0.891",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","467,0","0","467","0/1","306,17","0.0526","323",null,"chr9:71866951:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ABHD17B","chr9:71866951","ABHD17B(D235N)",null,null,"active site (Charge relay system )","active-site:Charge_relay_system","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Hydrolyzes fatty acids from S-acylated cysteine residues in proteins (PubMed:26701913). Has depalmitoylating activity towards DLG4/PSD95 (PubMed:26701913). Has depalmitoylating activity towards GAP43 (By similarity). Has depalmitoylating activity towards MAP6 (By similarity). Has depalmitoylating activity towards NRAS (PubMed:26701913). {ECO:0000250|UniProtKB:Q7M759, ECO:0000269|PubMed:26701913}.; ",{"$nulls":4},"p.Asp235Asn","c.703G>A","MODERATE","235/293",4,{"$nulls":5},"5","479","383","319","257","452","347","0","0","0","0.1326",{"$nulls":20},"4.105014","-1.99","4.905","1","-4.33","1.0","0.0","0.918;0.891",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","473,0","0","473","0/1","323,55","0.1455","378",null,"chr9:71866951:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1518"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ACVRL1","chr12:51919000","ACVRL1(Y435F)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Telangiectasia, hereditary hemorrhagic, 2 (HHT2) [MIM:600376]: A multisystemic vascular dysplasia leading to dilation of permanent blood vessels and arteriovenous malformations of skin, mucosa, and viscera. The disease is characterized by recurrent epistaxis and gastro-intestinal hemorrhage. Visceral involvement includes arteriovenous malformations of the lung, liver, and brain. {ECO:0000269|PubMed:10694922, ECO:0000269|PubMed:10767348, ECO:0000269|PubMed:11170071, ECO:0000269|PubMed:11484689, ECO:0000269|PubMed:14684682, ECO:0000269|PubMed:15024723, ECO:0000269|PubMed:15712270, ECO:0000269|PubMed:16525724, ECO:0000269|PubMed:16752392, ECO:0000269|PubMed:20414677, ECO:0000269|PubMed:26176610, ECO:0000269|PubMed:8640225, ECO:0000269|PubMed:9245985}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type I receptor for TGF-beta family ligands BMP9/GDF2 and BMP10 and important regulator of normal blood vessel development. On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. May bind activin as well. {ECO:0000269|PubMed:22718755, ECO:0000269|PubMed:22799562, ECO:0000269|PubMed:26176610}.; ","level2",{"$nulls":3},"p.Tyr435Phe","c.1304A>T","MODERATE","435/517",8,{"$nulls":5},"5","661","366","566","306","454","235","0","0","0","0.0681",{"$nulls":20},"4.181281","-3.19","1.625;.;.","1","-3.81;-3.81;-3.86","1.0;.;0.909","0.028;0.028;0.014","0.615;0.591;0.528",{"$nulls":3},"Unknown",-1,"AD","Hereditary hemorrhagic telangiectasia, type 2","Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Pulmonary",{"$nulls":3},"C1838163","0/0","643,0","0","643","0/1","337,20","0.056","357",null,"chr12:51919000:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0654"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ACVRL1","chr12:51919000","ACVRL1(Y435F)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Telangiectasia, hereditary hemorrhagic, 2 (HHT2) [MIM:600376]: A multisystemic vascular dysplasia leading to dilation of permanent blood vessels and arteriovenous malformations of skin, mucosa, and viscera. The disease is characterized by recurrent epistaxis and gastro-intestinal hemorrhage. Visceral involvement includes arteriovenous malformations of the lung, liver, and brain. {ECO:0000269|PubMed:10694922, ECO:0000269|PubMed:10767348, ECO:0000269|PubMed:11170071, ECO:0000269|PubMed:11484689, ECO:0000269|PubMed:14684682, ECO:0000269|PubMed:15024723, ECO:0000269|PubMed:15712270, ECO:0000269|PubMed:16525724, ECO:0000269|PubMed:16752392, ECO:0000269|PubMed:20414677, ECO:0000269|PubMed:26176610, ECO:0000269|PubMed:8640225, ECO:0000269|PubMed:9245985}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type I receptor for TGF-beta family ligands BMP9/GDF2 and BMP10 and important regulator of normal blood vessel development. On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. May bind activin as well. {ECO:0000269|PubMed:22718755, ECO:0000269|PubMed:22799562, ECO:0000269|PubMed:26176610}.; ","level2",{"$nulls":3},"p.Tyr435Phe","c.1304A>T","MODERATE","435/517",8,{"$nulls":5},"5","661","289","566","232","453","219","0","0","0","0.2192",{"$nulls":20},"4.181281","-3.19","1.625;.;.","1","-3.81;-3.81;-3.86","1.0;.;0.909","0.028;0.028;0.014","0.615;0.591;0.528",{"$nulls":3},"Unknown",-1,"AD","Hereditary hemorrhagic telangiectasia, type 2","Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Pulmonary",{"$nulls":3},"C1838163","0/0","643,0","0","643","0/1","235,49","0.1725","284",null,"chr12:51919000:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1638"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ADAMTS3","chr4:72319387","ADAMTS3(F433L)",null,null,"domain (Peptidase M12B ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cleaves the propeptides of type II collagen prior to fibril assembly. Does not act on types I and III collagens.; ",{"$nulls":4},"p.Phe433Leu","c.1297T>C","MODERATE","433/1205",9,{"$nulls":5},"4","1322","917","931","615","1205","823","0","0","0","0.1166",{"$nulls":20},"3.944686","-2.07;.","2.025","1","-5.37;.","0.995","0.013;.","0.833;0.811",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748408","0/0","1290,0","0","1290","0/1","779,103","0.1168","882",null,"chr4:72319387:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1138"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","AKAP6","chr14:32546377","AKAP6(S575*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the nuclear membrane or sarcoplasmic reticulum. May act as an adapter for assembling multiprotein complexes.; ",{"$nulls":4},"p.Ser575*","c.1724C>G","HIGH","575/2319",4,{"$nulls":5},"5","706","535","521","371","618","462","0","0","0","0.1212",{"$nulls":5},"(AKAP6|ENSG00000151320|1|1.00)","(AKAP6|ENSG00000151320|1|1.00)",{"$nulls":13},"6.72793",null,null,"1",{"$nulls":3},"0.907;0.932;0.913;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","700,0","0","700","0/1","433,68","0.1357","501",null,"chr14:32546377:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1267"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","AKAP6","chr14:32546377","AKAP6(S575*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the nuclear membrane or sarcoplasmic reticulum. May act as an adapter for assembling multiprotein complexes.; ",{"$nulls":4},"p.Ser575*","c.1724C>G","HIGH","575/2319",4,{"$nulls":5},"5","706","438","521","316","619","389","0","0","0","0.5013",{"$nulls":5},"(AKAP6|ENSG00000151320|1|1.00)","(AKAP6|ENSG00000151320|1|1.00)",{"$nulls":13},"6.72793",null,null,"1",{"$nulls":3},"0.907;0.932;0.913;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","701,0","0","701","0/1","215,212","0.4965","427",null,"chr14:32546377:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5127"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ALS2CL","chr3:46679275","ALS2CL(L521V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a guanine nucleotide exchange factor (GEF) for Rab5 GTPase. Regulates the ALS2-mediated endosome dynamics. {ECO:0000269|PubMed:15388334, ECO:0000269|PubMed:16473597, ECO:0000269|PubMed:17239822}.; ",{"$nulls":4},"p.Leu521Val","c.1561C>G","MODERATE","521/953",15,{"$nulls":5},"3",null,null,"340","224",{"$nulls":26},"3.419724","0.93","2.935","0.998352","-2.45","0.997","0.003","0.485;0.476",{"$nulls":3},"Unknown",-1,"AD","Schizophrenia","Neurologic",{"$nulls":4},"0/0","496,0","0","496","0/1","330,18","0.0517","348",null,"chr3:46679275:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ALS2CL","chr3:46679275","ALS2CL(L521V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a guanine nucleotide exchange factor (GEF) for Rab5 GTPase. Regulates the ALS2-mediated endosome dynamics. {ECO:0000269|PubMed:15388334, ECO:0000269|PubMed:16473597, ECO:0000269|PubMed:17239822}.; ",{"$nulls":4},"p.Leu521Val","c.1561C>G","MODERATE","521/953",15,{"$nulls":5},"5","496","140","340","97","440","130","0","0","0","0.1923",{"$nulls":20},"3.419724","0.93","2.935","0.998352","-2.45","0.997","0.003","0.485;0.476",{"$nulls":3},"Unknown",-1,"AD","Schizophrenia","Neurologic",{"$nulls":4},"0/0","478,0","0","478","0/1","108,27","0.2","135",null,"chr3:46679275:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2268"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ANHX","chr12:133227133","ANHX(T174M)",{"$nulls":6},255,"PASS","Missense","rs745417751",3.2179999999999996E-4,{"$nulls":6},"p.Thr174Met","c.521C>T","MODERATE","174/379",5,{"$nulls":5},"4","270","172","208","118","259","158","0","0","0","0.1646",{"$nulls":20},"2.89099","-3.97","3.035","0.986819","-5.16","1.0","0.0","0.196",{"$nulls":3},"ExAC_NFE_AF",3.2179999999999996E-4,{"$nulls":7},"0/0","271,0","0","271","0/1","140,26","0.1566","166",null,"chr12:133227133:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1441"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ANHX","chr12:133227133","ANHX(T174M)",{"$nulls":6},255,"PASS","Missense","rs745417751",3.2179999999999996E-4,{"$nulls":6},"p.Thr174Met","c.521C>T","MODERATE","174/379",5,{"$nulls":5},"4","270","151","208","110","259","139","0","0","0","0.5396",{"$nulls":20},"2.89099","-3.97","3.035","0.986819","-5.16","1.0","0.0","0.196",{"$nulls":3},"ExAC_NFE_AF",3.2179999999999996E-4,{"$nulls":7},"0/0","272,0","0","272","0/1","64,84","0.5676","148",null,"chr12:133227133:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5727"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ANTXR1","chr2:69102921","ANTXR1(I261M)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs1241426894",-1,"DISEASE: Hemangioma, capillary infantile (HCI) [MIM:602089]: A condition characterized by dull red, firm, dome-shaped hemangiomas, sharply demarcated from surrounding skin, usually presenting at birth or occurring within the first two or three months of life. They result from highly proliferative, localized growth of capillary endothelium and generally undergo regression and involution without scarring. {ECO:0000269|PubMed:18931684}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: GAPO syndrome (GAPO) [MIM:230740]: A disease characterized by growth retardation, alopecia, failure of tooth eruption, and progressive optic atrophy in some patients. {ECO:0000269|PubMed:23602711}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in cell attachment and migration. Interacts with extracellular matrix proteins and with the actin cytoskeleton. Mediates adhesion of cells to type 1 collagen and gelatin, reorganization of the actin cytoskeleton and promotes cell spreading. Plays a role in the angiogenic response of cultured umbilical vein endothelial cells. {ECO:0000269|PubMed:15777794, ECO:0000269|PubMed:16762926}.; ",{"$nulls":4},"p.Ile261Met","c.783C>G","MODERATE","261/564",10,{"$nulls":5},"5","553","325","372","215","516","302","0","0","0","0.1887",{"$nulls":20},"3.814852","-2.14","1.87","0.999859","-1.57;-1.54;-1.54","0.991;0.989;0.575","0.008;0.01;0.011","0.824;0.795;0.825",{"$nulls":3},"Unknown",-1,"AD/AR","Hemangioma, capillary infantile, susceptibility to; Growth retardation, alopecia, pseudoanodontia, and optic atrophy (GAPO syndrome)","Craniofacial; Dental; Dermatologic; Musculoskeletal; Ophthalmologic",{"$nulls":3},"C1865871| C0406723","0/0","536,0","0","536","0/1","254,61","0.1937","315",null,"chr2:69102921:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.186"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ARHGEF33","chr2:38931245","ARHGEF33(E167K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a guanine-nucleotide releasing factor. {ECO:0000250}.; ",{"$nulls":4},"p.Glu167Lys","c.499G>A","MODERATE","167/870",5,2,{"$nulls":4},"4","678","454","431","298","642","416","0","0","0","0.1947",{"$nulls":20},"2.695071","0.51","0.805","0.967918","-1.56",null,"0.0","0.512;0.487",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","664,0","0","664","0/1","358,83","0.1882","441",null,"chr2:38931245:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1913"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ARNTL","chr11:13372222","ARNTL(T294S)",null,null,"splice variant (In isoform BMAL1C. ), splice variant (In isoform BMAL1D. ), splice variant (In isoform BMAL1E. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time- keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK|NPAS2-ARNTL/BMAL1|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. ARNTL/BMAL1 positively regulates myogenesis and negatively regulates adipogenesis via the transcriptional control of the genes of the canonical Wnt signaling pathway. Plays a role in normal pancreatic beta-cell function; regulates glucose-stimulated insulin secretion via the regulation of antioxidant genes NFE2L2/NRF2 and its targets SESN2, PRDX3, CCLC and CCLM. Negatively regulates the mTORC1 signaling pathway; regulates the expression of MTOR and DEPTOR. Controls diurnal oscillations of Ly6C inflammatory monocytes; rhythmic recruitment of the PRC2 complex imparts diurnal variation to chemokine expression that is necessary to sustain Ly6C monocyte rhythms. Regulates the expression of HSD3B2, STAR, PTGS2, CYP11A1, CYP19A1 and LHCGR in the ovary and also the genes involved in hair growth. Plays an important role in adult hippocampal neurogenesis by regulating the timely entry of neural stem/progenitor cells (NSPCs) into the cell cycle and the number of cell divisions that take place prior to cell-cycle exit. Regulates the circadian expression of CIART and KLF11. The CLOCK-ARNTL/BMAL1 heterodimer regulates the circadian expression of SERPINE1/PAI1, VWF, B3, CCRN4L/NOC, NAMPT, DBP, MYOD1, PPARGC1A, PPARGC1B, SIRT1, GYS2, F7, NGFR, GNRHR, BHLHE40/DEC1, ATF4, MTA1, KLF10 and also genes implicated in glucose and lipid metabolism. Promotes rhythmic chromatin opening, regulating the DNA accessibility of other transcription factors. The NPAS2-ARNTL/BMAL1 heterodimer positively regulates the expression of MAOA, F7 and LDHA and modulates the circadian rhythm of daytime contrast sensitivity by regulating the rhythmic expression of adenylate cyclase type 1 (ADCY1) in the retina. The preferred binding motif for the CLOCK- ARNTL/BMAL1 heterodimer is 5'-CACGTGA-3', which contains a flanking Ala residue in addition to the canonical 6-nucleotide E- box sequence (PubMed:23229515). CLOCK specifically binds to the half-site 5'-CAC-3', while ARNTL binds to the half-site 5'-GTGA-3' (PubMed:23229515). The CLOCK-ARNTL/BMAL1 heterodimer also recognizes the non-canonical E-box motifs 5'-AACGTGA-3' and 5'- CATGTGA-3' (PubMed:23229515). Essential for the rhythmic interaction of CLOCK with ASS1 and plays a critical role in positively regulating CLOCK-mediated acetylation of ASS1 (PubMed:28985504). {ECO:0000269|PubMed:11441146, ECO:0000269|PubMed:12738229, ECO:0000269|PubMed:18587630, ECO:0000269|PubMed:23785138, ECO:0000269|PubMed:23955654, ECO:0000269|PubMed:24005054, ECO:0000269|PubMed:28985504}.; ",{"$nulls":4},"p.Thr294Ser","c.880A>T","MODERATE","294/626",13,{"$nulls":5},"4","553","312","467","244","444","251","0","0","0","0.2749",{"$nulls":20},"1.986177","3.16;3.15;3.15;3.16;3.14",".;.;-0.76;.;.","1","0.61","0.013;0.001;0.001;.;0.003","0.715;0.85;0.72;0.853;0.514","0.468;0.474;0.459;0.471;0.451",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","538,0","0","538","0/1","215,81","0.2736","296",null,"chr11:13372222:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2623"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ASB18","chr2:236196315","ASB18(L391*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000250}.; ",{"$nulls":4},"p.Leu391*","c.1172T>A","HIGH","391/466",5,{"$nulls":5},"5","581","188","408","138","520","154","0","0","0","0.2987",{"$nulls":20},"8.101565",null,null,"1",{"$nulls":3},".;0.172;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","567,0","0","567","0/1","131,56","0.2995","187",null,"chr2:236196315:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.2899"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ASXL1","chr20:32436728","ASXL1(G1339A)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Bohring-Opitz syndrome (BOPS) [MIM:605039]: A syndrome characterized by severe intrauterine growth retardation, poor feeding, profound mental retardation, trigonocephaly, prominent metopic suture, exophthalmos, nevus flammeus of the face, upslanting palpebral fissures, hirsutism, and flexion of the elbows and wrists with deviation of the wrists and metacarpophalangeal joints. {ECO:0000269|PubMed:21706002}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myelodysplastic syndrome (MDS) [MIM:614286]: A heterogeneous group of closely related clonal hematopoietic disorders. All are characterized by a hypercellular or hypocellular bone marrow with impaired morphology and maturation, dysplasia of the myeloid, megakaryocytic and/or erythroid lineages, and peripheral blood cytopenias resulting from ineffective blood cell production. Included diseases are: refractory anemia (RA), refractory anemia with ringed sideroblasts (RARS), refractory anemia with excess blasts (RAEB), refractory cytopenia with multilineage dysplasia and ringed sideroblasts (RCMD-RS); chronic myelomonocytic leukemia (CMML) is a myelodysplastic/myeloproliferative disease. MDS is considered a premalignant condition in a subgroup of patients that often progresses to acute myeloid leukemia (AML). {ECO:0000269|PubMed:19388938, ECO:0000269|PubMed:20182461}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Probable Polycomb group (PcG) protein involved in transcriptional regulation mediated by ligand-bound nuclear hormone receptors, such as retinoic acid receptors (RARs) and peroxisome proliferator-activated receptor gamma (PPARG). Acts as coactivator of RARA and RXRA through association with NCOA1. Acts as corepressor for PPARG and suppresses its adipocyte differentiation-inducing activity (By similarity). Non-catalytic component of the PR-DUB complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-119' (H2AK119ub1). {ECO:0000250, ECO:0000269|PubMed:16606617, ECO:0000269|PubMed:20436459}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Gly1339Ala","c.4016G>C","MODERATE","1339/1541",13,{"$nulls":5},"4","770","507","603","394","678","432","0.0013","0.0013","0","0.1389",{"$nulls":20},"1.372193","2.63;.;.;.;2.63","1.6;1.6;1.6;.;.","1","0.45;.;.;.;0.45","0.278;0.278;0.278;.;.","0.371;.;.;.;0.367","0.103;0.081;0.093;.;0.071",{"$nulls":3},"Unknown",-1,"AD","Bohring-Opitz syndrome","Craniofacial; Dermatologic; Musculoskeletal; Neurologic","COSMIC",null,null,"C0796232| C3463824","0/0","761,1","0.0013","762","0/1","427,71","0.1426","498",null,"chr20:32436728:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1523"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","BECN1","chr17:42810799","BECN1(W438C)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Plays a central role in autophagy (PubMed:23184933, PubMed:28445460). Acts as core subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123, PubMed:20208530, PubMed:26783301). Essential for the formation of PI3KC3-C2 but not PI3KC3-C1 PI3K complex forms. Involved in endocytosis (PubMed:25275521). Protects against infection by a neurovirulent strain of Sindbis virus (PubMed:9765397). May play a role in antiviral host defense. {ECO:0000269|PubMed:20208530, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:23184933, ECO:0000269|PubMed:25275521, ECO:0000269|PubMed:26783301, ECO:0000269|PubMed:28445460, ECO:0000269|PubMed:9765397, ECO:0000305}.; ","level2","[ \"Bortezomib\"]","[ \"Bortezomib\"]","[ \"Bortezomib\"]",null,"c.1314G>T","HIGH",null,12,{"$nulls":5},"4","617","419","448","298","534","369","0","0","0","0.0813",{"$nulls":20},"3.7868690000000003","0.71","3.02;3.02;.","1","-9.75;.;.","1.0;1.0;.","0.097;.;.","0.882;0.88;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kREGULATION_OF_AUTOPHAGY",{"$nulls":3},"0/0","609,0","0","609","0/1","371,37","0.0907","408",null,"chr17:42810799:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.094"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","BECN1","chr17:42810799","BECN1(W438C)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Plays a central role in autophagy (PubMed:23184933, PubMed:28445460). Acts as core subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123, PubMed:20208530, PubMed:26783301). Essential for the formation of PI3KC3-C2 but not PI3KC3-C1 PI3K complex forms. Involved in endocytosis (PubMed:25275521). Protects against infection by a neurovirulent strain of Sindbis virus (PubMed:9765397). May play a role in antiviral host defense. {ECO:0000269|PubMed:20208530, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:23184933, ECO:0000269|PubMed:25275521, ECO:0000269|PubMed:26783301, ECO:0000269|PubMed:28445460, ECO:0000269|PubMed:9765397, ECO:0000305}.; ","level2","[ \"Bortezomib\"]","[ \"Bortezomib\"]","[ \"Bortezomib\"]",null,"c.1314G>T","HIGH",null,12,{"$nulls":5},"4","617","343","448","252","530","274","0","0","0","0.4234",{"$nulls":20},"3.7868690000000003","0.71","3.02;3.02;.","1","-9.75;.;.","1.0;1.0;.","0.097;.;.","0.882;0.88;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kREGULATION_OF_AUTOPHAGY",{"$nulls":3},"0/0","601,0","0","601","0/1","190,143","0.4294","333",null,"chr17:42810799:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4286"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","BEST2","chr19:12757721","BEST2(D392N)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Forms calcium-sensitive chloride channels. Permeable to bicarbonate. {ECO:0000269|PubMed:11904445, ECO:0000269|PubMed:12907679, ECO:0000269|PubMed:18400985}.; ",{"$nulls":4},"p.Asp392Asn","c.1174G>A","MODERATE","392/509",9,{"$nulls":5},"4","398","207","329","170","314","179","0","0","0","0.0782",{"$nulls":20},"2.773116","-4.63","1.95","0.596545","0.34","0.111","0.196","0.242;0.248;0.241",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","393,0","0","393","0/1","186,14","0.07","200",null,"chr19:12757721:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0765"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","BEX4","chrX:103216488","BEX4(N112S)",null,null,"region of interest (Interaction with alpha-tubulin )",{"$nulls":3},255,"PASS","Missense","rs766131210",1.076E-4,null,"FUNCTION: May play a role in microtubule deacetylation by negatively regulating the SIRT2 deacetylase activity toward alpha- tubulin and thereby participate to the control of cell cycle progression and genomic stability. {ECO:0000269|PubMed:27512957}.; ",{"$nulls":4},"p.Asn112Ser","c.335A>G","MODERATE","112/120",2,1,{"$nulls":4},"5","725","392","531","265","640","321","0","0","0","0.1651",{"$nulls":20},"3.14939","0.06","1.79","0.971789","-3.07","0.945","0.12","0.212;0.213",{"$nulls":3},"ExAC_AMR_AF",1.076E-4,{"$nulls":7},"0/0","701,0","0","701","0/1","319,61","0.1605","380",null,"chrX:103216488:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1623"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","BMPR1B","chr4:95131499","BMPR1B(V385L)",{"$nulls":6},255,"PASS","Missense","rs1224854340",-1,"DISEASE: Acromesomelic dysplasia, Demirhan type (AMDD) [MIM:609441]: A form of chondrodysplasia. Acromesomelic chondrodysplasias are rare hereditary skeletal disorders characterized by short stature, very short limbs and hand/foot malformations. The severity of limb abnormalities increases from proximal to distal with profoundly affected hands and feet showing brachydactyly and/or rudimentary fingers (knob-like fingers). AMDD inheritance is autosomal recessive. {ECO:0000269|PubMed:15805157, ECO:0000269|PubMed:24129431, ECO:0000269|PubMed:26105076}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brachydactyly A2 (BDA2) [MIM:112600]: A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. In brachydactyly type A2 shortening of the middle phalanges is confined to the index finger and the second toe, all other digits being more or less normal. Because of a rhomboid or triangular shape of the affected middle phalanx, the end of the second finger usually deviates radially. {ECO:0000269|PubMed:14523231, ECO:0000269|PubMed:16957682}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brachydactyly A1, D (BDA1D) [MIM:616849]: A form of brachydactyly type A1. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type A1 is characterized by middle phalanges of all the digits rudimentary or fused with the terminal phalanges. The proximal phalanges of the thumbs and big toes are short. BDA1D inheritance is autosomal dominant. {ECO:0000269|PubMed:25758993}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Receptor for BMP7/OP-1 and GDF5. Positively regulates chondrocyte differentiation through GDF5 interaction. {ECO:0000250|UniProtKB:P36898}.; ","level2",{"$nulls":3},"p.Val385Leu","c.1153G>C","MODERATE","385/532",8,{"$nulls":5},"5","448","255","345","185","430","245","0","0","0","0.0694",{"$nulls":20},"4.094","-3.19","0.545;0.545;.;0.545;0.545","1","-2.88","0.994;0.994;.;0.994;0.994","0.001","0.763;0.801;0.76;0.759;0.762",{"$nulls":3},"Unknown",-1,"AD/AR","Chondrodysplasia, acromesomelic, with genital anomalies; Brachydactyly A2; Brachydactyly C/Symphalangism-like phenotype","Genitourinary; Musculoskeletal","kTGF_BETA",null,null,"C4225183| C1832702| C4225404","0/0","446,0","0","446","0/1","237,19","0.0742","256",null,"chr4:95131499:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0703"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","BMPR1B","chr4:95131499","BMPR1B(V385L)",{"$nulls":6},255,"PASS","Missense","rs1224854340",-1,"DISEASE: Acromesomelic dysplasia, Demirhan type (AMDD) [MIM:609441]: A form of chondrodysplasia. Acromesomelic chondrodysplasias are rare hereditary skeletal disorders characterized by short stature, very short limbs and hand/foot malformations. The severity of limb abnormalities increases from proximal to distal with profoundly affected hands and feet showing brachydactyly and/or rudimentary fingers (knob-like fingers). AMDD inheritance is autosomal recessive. {ECO:0000269|PubMed:15805157, ECO:0000269|PubMed:24129431, ECO:0000269|PubMed:26105076}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brachydactyly A2 (BDA2) [MIM:112600]: A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. In brachydactyly type A2 shortening of the middle phalanges is confined to the index finger and the second toe, all other digits being more or less normal. Because of a rhomboid or triangular shape of the affected middle phalanx, the end of the second finger usually deviates radially. {ECO:0000269|PubMed:14523231, ECO:0000269|PubMed:16957682}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brachydactyly A1, D (BDA1D) [MIM:616849]: A form of brachydactyly type A1. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type A1 is characterized by middle phalanges of all the digits rudimentary or fused with the terminal phalanges. The proximal phalanges of the thumbs and big toes are short. BDA1D inheritance is autosomal dominant. {ECO:0000269|PubMed:25758993}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Receptor for BMP7/OP-1 and GDF5. Positively regulates chondrocyte differentiation through GDF5 interaction. {ECO:0000250|UniProtKB:P36898}.; ","level2",{"$nulls":3},"p.Val385Leu","c.1153G>C","MODERATE","385/532",8,{"$nulls":5},"5","448","240","345","181","429","225","0","0","0","0.1556",{"$nulls":20},"4.094","-3.19","0.545;0.545;.;0.545;0.545","1","-2.88","0.994;0.994;.;0.994;0.994","0.001","0.763;0.801;0.76;0.759;0.762",{"$nulls":3},"Unknown",-1,"AD/AR","Chondrodysplasia, acromesomelic, with genital anomalies; Brachydactyly A2; Brachydactyly C/Symphalangism-like phenotype","Genitourinary; Musculoskeletal","kTGF_BETA",null,null,"C4225183| C1832702| C4225404","0/0","443,0","0","443","0/1","184,38","0.1712","222",null,"chr4:95131499:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1657"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","BNC1","chr15:83263275","BNC1(M644_F658del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Transcriptional activator (By similarity). Likely specific for squamous epithelium and for the constituent keratinocytes at a stage either prior to or at the very beginning of terminal differentiation (PubMed:8034748). Required for the maintenance of spermatogenesis (By similarity). May also play a role in the differentiation of oocytes and the early development of embryos (By similarity). {ECO:0000250|UniProtKB:O35914, ECO:0000269|PubMed:8034748}.; ",{"$nulls":4},"p.Met644_Phe658del","c.1931_1975delTGGTGCCAAGGGAGGTCGAGGATGGTGGCCATGAACACTACTTCA","MODERATE","644/994",4,{"$nulls":5},"3",null,null,"704","553","859","767",null,null,"0","0.1199",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C5231474","0/0","1273,0","0","1273","0/1","913,82","0.0824","995",null,"chr15:83263275:GTGAAGTAGTGTTCATGGCCACCATCCTCGACCTCCCTTGGCACCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1175"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","BROX","chr1:222719320","BROX(N89I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asn89Ile","c.266A>T","MODERATE","89/411",4,{"$nulls":5},"5","281","189","195","132","247","168","0","0","0","0.125",{"$nulls":20},"2.481382","2.26;.;.;2.26;2.26","2.2;2.2;2.2;.;.","1","-1.12;.;-1.42;-1.42;-1.43","0.057;.;.;0.046;.","0.096;.;0.107;0.144;0.381","0.815;0.835;0.835;0.812;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","277,0","0","277","0/1","156,26","0.1429","182",null,"chr1:222719320:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1288"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","C21orf62","chr21:32810586","C21orf62(C56S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Cys56Ser","c.167G>C","MODERATE","56/266",2,{"$nulls":5},"4","812","583","662","441","584","417","0","0","0","0.0911",{"$nulls":20},"0.324111",null,null,"1;0.999993;1;0.999993","0.99",null,"0.073",{"$nulls":4},"Unknown",-1,{"$nulls":7},"0/0","804,0","0","804","0/1","520,38","0.0681","558",null,"chr21:32810586:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0703"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","C21orf62","chr21:32810586","C21orf62(C56S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Cys56Ser","c.167G>C","MODERATE","56/266",2,{"$nulls":5},"4","812","516","662","411","584","388","0","0","0","0.3222",{"$nulls":20},"0.324111",null,null,"1;0.999993;1;0.999993","0.99",null,"0.073",{"$nulls":4},"Unknown",-1,{"$nulls":7},"0/0","808,0","0","808","0/1","349,153","0.3048","502",null,"chr21:32810586:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3041"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CACHD1","chr1:64663747","CACHD1(H617Q)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May regulate voltage-dependent calcium channels. {ECO:0000250}.; ",{"$nulls":4},"p.His617Gln","c.1851C>A","MODERATE","617/1223",14,{"$nulls":5},"4","1090","708","787","489","935","592","0.0018","0.0018","0","0.0895",{"$nulls":20},"3.098792","1.92;.",null,"1","-3.22;.",null,"0.006;.","0.813;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1061,2","0.0019","1063","0/1","587,68","0.1038","655",null,"chr1:64663747:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0941"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CACHD1","chr1:64663747","CACHD1(H617Q)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May regulate voltage-dependent calcium channels. {ECO:0000250}.; ",{"$nulls":4},"p.His617Gln","c.1851C>A","MODERATE","617/1223",14,{"$nulls":5},"4","1090","649","787","452","931","560","0.0018","0.0018","0","0.3071",{"$nulls":20},"3.098792","1.92;.",null,"1","-3.22;.",null,"0.006;.","0.813;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1055,2","0.0019","1057","0/1","420,196","0.3182","616",null,"chr1:64663747:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3097"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CACNA1C","chr12:2457568","CACNA1C(L207I)",null,null,"transmembrane region (Helical; Name=S3 of repeat I ), repeat (I )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Timothy syndrome (TS) [MIM:601005]: Disorder characterized by multiorgan dysfunction including lethal arrhythmias, webbing of fingers and toes, congenital heart disease, immune deficiency, intermittent hypoglycemia, cognitive abnormalities and autism. {ECO:0000269|PubMed:15454078, ECO:0000269|PubMed:15863612, ECO:0000269|PubMed:24728418, ECO:0000269|PubMed:25260352, ECO:0000269|PubMed:25633834, ECO:0000269|PubMed:26253506}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brugada syndrome 3 (BRGDA3) [MIM:611875]: A heart disease characterized by the association of Brugada syndrome with shortened QT intervals. Brugada syndrome is a tachyarrhythmia characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will faint and may die in a few minutes if the heart is not reset. {ECO:0000269|PubMed:17224476}. Note=The gene represented in this entry may be involved in disease pathogenesis.; ","FUNCTION: Pore-forming, alpha-1C subunit of the voltage-gated calcium channel that gives rise to L-type calcium currents (PubMed:8392192, PubMed:7737988, PubMed:9087614, PubMed:9013606, PubMed:9607315, PubMed:12176756, PubMed:17071743, PubMed:11741969, PubMed:8099908, PubMed:12181424, PubMed:29078335, PubMed:29742403, PubMed:16299511, PubMed:20953164, PubMed:15454078, PubMed:15863612, PubMed:17224476, PubMed:24728418, PubMed:26253506, PubMed:27218670). Mediates influx of calcium ions into the cytoplasm, and thereby triggers calcium release from the sarcoplasm (By similarity). Plays an important role in excitation- contraction coupling in the heart. Required for normal heart development and normal regulation of heart rhythm (PubMed:15454078, PubMed:15863612, PubMed:17224476, PubMed:24728418, PubMed:26253506). Required for normal contraction of smooth muscle cells in blood vessels and in the intestine. Essential for normal blood pressure regulation via its role in the contraction of arterial smooth muscle cells (PubMed:28119464). Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group (Probable). {ECO:0000250|UniProtKB:P15381, ECO:0000269|PubMed:11741969, ECO:0000269|PubMed:12176756, ECO:0000269|PubMed:12181424, ECO:0000269|PubMed:15454078, ECO:0000269|PubMed:15863612, ECO:0000269|PubMed:16299511, ECO:0000269|PubMed:17071743, ECO:0000269|PubMed:17224476, ECO:0000269|PubMed:20953164, ECO:0000269|PubMed:24728418, ECO:0000269|PubMed:26253506, ECO:0000269|PubMed:27218670, ECO:0000269|PubMed:28119464, ECO:0000269|PubMed:29078335, ECO:0000269|PubMed:29742403, ECO:0000269|PubMed:7737988, ECO:0000269|PubMed:8099908, ECO:0000269|PubMed:8392192, ECO:0000269|PubMed:9013606, ECO:0000269|PubMed:9087614, ECO:0000269|PubMed:9607315, ECO:0000305}.; ","acmg|level2",{"$nulls":3},"p.Leu207Ile","c.619C>A","MODERATE","207/2209",5,{"$nulls":5},"4","421","638","337","493","313","482","0","0","0","0.0913",{"$nulls":20},"4.08066","-4.91",".;1.135;.;1.135;1.135;1.135;1.135;1.135;1.135;1.135;1.135;1.135;1.135;1.135;1.135;1.135;.;1.135;1.135;1.135;.;.;.","0.999975","-1.18;-1.18;-1.16;-1.15;-1.18;-1.21;-1.18;-1.18;-1.18;-1.15;-1.18;-1.21;-1.18;-1.18;-1.18;-1.18;-1.18;-1.15;-1.18;-1.18;-1.21;-1.18;-1.21",".;0.99;.;0.816;1.0;0.914;0.99;0.999;0.999;0.94;0.996;0.999;0.999;0.99;0.992;0.999;.;0.999;0.999;.;.;.;.","0.055;0.055;0.05;0.056;0.056;0.055;0.055;0.056;0.056;0.056;0.055;0.057;0.057;0.056;0.055;0.057;0.055;0.057;0.055;0.056;0.054;0.054;0.054","0.591;0.658;0.615;0.653;0.659;0.637;0.66;0.661;0.657;0.663;0.643;0.64;0.663;0.658;0.6;0.662;0.611;0.658;0.644;0.654;0.655;0.659;0.649",{"$nulls":3},"Unknown",-1,"AD","Brugada syndrome 3; Timothy syndrome","Allergy/Immunology/Infectious; Cardiovascular; Musculoskeletal; Neurologic ","kMAPK",null,null,"C1832916| C2678478| CN260585","0/0","412,0","0","412","0/1","576,45","0.0725","621",null,"chr12:2457568:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CACNA1H","chr16:1216946","CACNA1H(L1754F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Epilepsy, idiopathic generalized 6 (EIG6) [MIM:611942]: A disorder characterized by recurring generalized seizures in the absence of detectable brain lesions and/or metabolic abnormalities. Generalized seizures arise diffusely and simultaneously from both hemispheres of the brain. {ECO:0000269|PubMed:15048902}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Epilepsy, childhood absence 6 (ECA6) [MIM:611942]: A subtype of idiopathic generalized epilepsy characterized by an onset at age 6-7 years, frequent absence seizures (several per day) and bilateral, synchronous, symmetric 3-Hz spike waves on EEG. Tonic-clonic seizures often develop in adolescence. Absence seizures may either remit or persist into adulthood. {ECO:0000269|PubMed:12891677}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hyperaldosteronism, familial, 4 (HALD4) [MIM:617027]: A form of familial hyperaldosteronism, a disorder characterized by hypertension, elevated aldosterone levels despite low plasma renin activity, and abnormal adrenal steroid production. There is significant phenotypic heterogeneity, and some individuals never develop hypertension. {ECO:0000269|PubMed:25907736, ECO:0000269|PubMed:27729216}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Voltage-sensitive calcium channel that gives rise to T- type calcium currents. T-type calcium channels belong to the \"low- voltage activated (LVA)\" group. A particularity of this type of channel is an opening at quite negative potentials, and a voltage- dependent inactivation (PubMed:9670923, PubMed:9930755, PubMed:27149520). T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle (Probable). They may also be involved in the modulation of firing patterns of neurons (PubMed:15048902). In the adrenal zona glomerulosa, participates in the signaling pathway leading to aldosterone production in response to either AGT/angiotensin II, or hyperkalemia (PubMed:25907736, PubMed:27729216). {ECO:0000269|PubMed:25907736, ECO:0000269|PubMed:27149520, ECO:0000269|PubMed:27729216, ECO:0000269|PubMed:9670923, ECO:0000269|PubMed:9930755, ECO:0000305, ECO:0000305|PubMed:15048902}.; ","gedi|level2",{"$nulls":3},"p.Leu1754Phe","c.5259_5260delCCinsAT","MODERATE","1753/2353",31,{"$nulls":5},"4","375","221","265","157","328","186","0","0","0","0.0699",{"$nulls":31},"Unknown",-1,{"$nulls":3},"kMAPK",null,null,"C2749872| C4310756","0/0","361,0","0","361","0/1","184,18","0.0891","202",null,"chr16:1216946:CC:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0955"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CAPN2","chr1:223752883","CAPN2(K354K)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs1172087442",-1,null,"FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. Proteolytically cleaves MYOC at 'Arg-226' (PubMed:17650508). Proteolytically cleaves CPEB3 following neuronal stimulation which abolishes CPEB3 translational repressor activity, leading to translation of CPEB3 target mRNAs (By similarity). {ECO:0000250|UniProtKB:O08529, ECO:0000269|PubMed:17650508}.; ","level2",{"$nulls":4},"c.1062G>A","HIGH",null,9,1,{"$nulls":4},"4","516","413","353","272","430","337","0","0","0","0.095",{"$nulls":31},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS",{"$nulls":3},"0/0","504,0","0","504","0/1","347,48","0.1215","395",null,"chr1:223752883:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1176"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CAPN2","chr1:223752883","CAPN2(K354K)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs1172087442",-1,null,"FUNCTION: Calcium-regulated non-lysosomal thiol-protease which catalyzes limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction. Proteolytically cleaves MYOC at 'Arg-226' (PubMed:17650508). Proteolytically cleaves CPEB3 following neuronal stimulation which abolishes CPEB3 translational repressor activity, leading to translation of CPEB3 target mRNAs (By similarity). {ECO:0000250|UniProtKB:O08529, ECO:0000269|PubMed:17650508}.; ","level2",{"$nulls":4},"c.1062G>A","HIGH",null,9,1,{"$nulls":4},"4","516","375","353","252","433","299","0","0","0","0.4415",{"$nulls":31},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS",{"$nulls":3},"0/0","504,0","0","504","0/1","190,170","0.4722","360",null,"chr1:223752883:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4603"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CATSPERB","chr14:91693398","CATSPERB(Y232fs)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Probably involved in sperm cell hyperactivation via its association with CATSPER1. Sperm cell hyperactivation is needed for sperm motility which is essential late in the preparation of sperm for fertilization. {ECO:0000250|UniProtKB:A2RTF1}.; ",{"$nulls":4},"p.Tyr232fs","c.694_697delTATT","HIGH","232/1116",8,{"$nulls":5},"4","652","366","485","251","583","319","0","0","0","0.094",{"$nulls":5},"(CATSPERB|ENSG00000133962|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","656,0","0","656","0/1","310,34","0.0988","344",null,"chr14:91693398:GAATA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0996"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CATSPERB","chr14:91693398","CATSPERB(Y232fs)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Probably involved in sperm cell hyperactivation via its association with CATSPER1. Sperm cell hyperactivation is needed for sperm motility which is essential late in the preparation of sperm for fertilization. {ECO:0000250|UniProtKB:A2RTF1}.; ",{"$nulls":4},"p.Tyr232fs","c.694_697delTATT","HIGH","232/1116",8,{"$nulls":5},"4","652","290","485","197","584","257","0","0","0","0.3696",{"$nulls":5},"(CATSPERB|ENSG00000133962|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","656,0","0","656","0/1","169,107","0.3877","276",null,"chr14:91693398:GAATA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3807"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CCDC127","chr5:205671","CCDC127(K112fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Lys112fs","c.336_408delGTTGGTAGAAGAAAAGAAGCTTCTGGAACAGGAACGGGCCCAGGTGATGCAAGAAAAAAGACAGGTGCAGCCT","HIGH","112/260",3,{"$nulls":20},"205744",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr5:205671:AAGGCTGCACCTGTCTTTTTTCTTGCATCACCTGGGCCCGTTCCTGTTCCAGAAGCTTCTTTTCTTCTACCAAC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CCDC127","chr5:205671","CCDC127(K112fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Lys112fs","c.336_408delGTTGGTAGAAGAAAAGAAGCTTCTGGAACAGGAACGGGCCCAGGTGATGCAAGAAAAAAGACAGGTGCAGCCT","HIGH","112/260",3,{"$nulls":20},"205744",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr5:205671:AAGGCTGCACCTGTCTTTTTTCTTGCATCACCTGGGCCCGTTCCTGTTCCAGAAGCTTCTTTTCTTCTACCAAC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CCDC127","chr5:205671","CCDC127(K112fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Lys112fs","c.336_408delGTTGGTAGAAGAAAAGAAGCTTCTGGAACAGGAACGGGCCCAGGTGATGCAAGAAAAAAGACAGGTGCAGCCT","HIGH","112/260",3,{"$nulls":5},"3",null,null,"743","370","799","513",null,null,"0","0.193",{"$nulls":5},"(CCDC127|ENSG00000164366|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","1646,0","0","1646","0/1","799,91","0.1022","890",null,"chr5:205671:AAGGCTGCACCTGTCTTTTTTCTTGCATCACCTGGGCCCGTTCCTGTTCCAGAAGCTTCTTTTCTTCTACCAAC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2027"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CCDC137","chr17:81672612","CCDC137(Q269*)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gln269*","c.805C>T","HIGH","269/291",7,{"$nulls":5},"4","585","303","408","215","514","278","0","0","0","0.1259",{"$nulls":20},"8.141006",null,null,"1",{"$nulls":3},"0.037;.",{"$nulls":3},"Unknown",-1,"AD","Schizophrenia","Neurologic",{"$nulls":4},"0/0","575,0","0","575","0/1","255,41","0.1385","296",null,"chr17:81672612:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1488"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CCHCR1","chr6:31154672","CCHCR1(M209L)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs1202778941",-1,null,"FUNCTION: May be a regulator of keratinocyte proliferation or differentiation.; ",{"$nulls":4},"p.Met209Leu","c.625A>T","MODERATE","209/871",4,{"$nulls":5},"4","569","405","436","294","504","364","0","0","0","0.0797",{"$nulls":20},"1.821805","3.93",".;1.355;.;.;.;.;.;.;.;.;.;.","0.997264","-0.76;-0.7;-0.51;-0.7;-1.53;-1.5;-1.31;-1.83;-1.83;-1.69;-1.69;-1.69","0.002;0.003;.;.;.;.;.;.;.;.;.;.","0.253;0.361;0.136;0.22;0.113;0.111;0.123;0.136;0.149;0.171;0.171;0.181","0.189;0.172;0.203;0.226;.;.;.;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","562,0","0","562","0/1","358,34","0.0867","392",null,"chr6:31154672:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0986"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CCHCR1","chr6:31154672","CCHCR1(M209L)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense","rs1202778941",-1,null,"FUNCTION: May be a regulator of keratinocyte proliferation or differentiation.; ",{"$nulls":4},"p.Met209Leu","c.625A>T","MODERATE","209/871",4,{"$nulls":5},"4","569","290","436","228","504","255","0","0","0","0.3294",{"$nulls":20},"1.821805","3.93",".;1.355;.;.;.;.;.;.;.;.;.;.","0.997264","-0.76;-0.7;-0.51;-0.7;-1.53;-1.5;-1.31;-1.83;-1.83;-1.69;-1.69;-1.69","0.002;0.003;.;.;.;.;.;.;.;.;.;.","0.253;0.361;0.136;0.22;0.113;0.111;0.123;0.136;0.149;0.171;0.171;0.181","0.189;0.172;0.203;0.226;.;.;.;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","562,0","0","562","0/1","186,97","0.3428","283",null,"chr6:31154672:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3465"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CCSAP","chr1:229342264","CCSAP(G68R)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in microtubule (MT) stabilization and this stabilization involves the maintenance of NUMA1 at the spindle poles. Colocalizes with polyglutamylated MTs to promote MT stabilization and regulate bipolar spindle formation in mitosis. Binding of CCSAP to centrosomes and the spindle around centrosomes during mitosis inhibits MT depolymerization, thereby stabilizing the mitotic spindle (PubMed:26562023). May play a role in embryonic development. May be required for proper cilia beating (By similarity). {ECO:0000250|UniProtKB:Q6P3G4, ECO:0000269|PubMed:26562023}.; ",{"$nulls":4},"p.Gly68Arg","c.202G>C","MODERATE","68/270",2,{"$nulls":5},"5","185","75","174","70","144","57","0","0","0","0.0877",{"$nulls":20},"1.5622289999999999","1.0","0.425","0.999999;0.999999;1","-2.05","0.904","0.017","0.139;0.143",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,0","0","181","0/1","64,6","0.0857","70",null,"chr1:229342264:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0714"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CCSAP","chr1:229342264","CCSAP(G68R)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in microtubule (MT) stabilization and this stabilization involves the maintenance of NUMA1 at the spindle poles. Colocalizes with polyglutamylated MTs to promote MT stabilization and regulate bipolar spindle formation in mitosis. Binding of CCSAP to centrosomes and the spindle around centrosomes during mitosis inhibits MT depolymerization, thereby stabilizing the mitotic spindle (PubMed:26562023). May play a role in embryonic development. May be required for proper cilia beating (By similarity). {ECO:0000250|UniProtKB:Q6P3G4, ECO:0000269|PubMed:26562023}.; ",{"$nulls":4},"p.Gly68Arg","c.202G>C","MODERATE","68/270",2,{"$nulls":5},"5","185","86","174","86","142","60","0","0","0","0.4333",{"$nulls":20},"1.5622289999999999","1.0","0.425","0.999999;0.999999;1","-2.05","0.904","0.017","0.139;0.143",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,0","0","181","0/1","46,37","0.4458","83",null,"chr1:229342264:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4302"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CCT3","chr1:156318878","CCT3(G250E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.; ",{"$nulls":4},"p.Gly250Glu","c.749G>A","MODERATE","250/545",8,{"$nulls":5},"5","403","288","344","244","319","220","0","0","0","0.1818",{"$nulls":20},"3.983162","-1.01","1.835;.;.;.","1","-7.62;-7.63;-7.63;-7.43","1.0;0.998;.;.","0.001","0.867;0.833;0.835;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","403,0","0","403","0/1","241,41","0.1454","282",null,"chr1:156318878:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1434"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CDKL2","chr4:75614394","CDKL2(R75Q)",{"$nulls":6},255,"PASS","Missense","rs751297970",1.501E-5,{"$nulls":6},"p.Arg75Gln","c.224G>A","MODERATE","75/570",3,{"$nulls":5},"4","444","312","289","198","389","271","0","0","0","0.155",{"$nulls":20},"3.625722","-0.14","0.645;.","0.997762","-2.64","0.987;.","0.003;0.004","0.6;0.613",{"$nulls":3},"ExAC_NFE_AF",1.501E-5,{"$nulls":4},"This gene product is a member of a large family of CDC2-related serine/threonine protein kinases. It accumulates primarily in the cytoplasm, with lower levels in the nucleus. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","425,0","0","425","0/1","251,51","0.1689","302",null,"chr4:75614394:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1515"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CENPF","chr1:214657286","CENPF(P2947S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Stromme syndrome (STROMS) [MIM:243605]: An autosomal recessive congenital disorder characterized by intestinal atresia, ocular anomalies, microcephaly, and renal and cardiac abnormalities in some patients. The disease has features of a ciliopathy, and lethality in early childhood is observed in severe cases. {ECO:0000269|PubMed:25564561, ECO:0000269|PubMed:26820108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for kinetochore function and chromosome segregation in mitosis. Required for kinetochore localization of dynein, LIS1, NDE1 and NDEL1. Regulates recycling of the plasma membrane by acting as a link between recycling vesicles and the microtubule network though its association with STX4 and SNAP25. Acts as a potential inhibitor of pocket protein-mediated cellular processes during development by regulating the activity of RB proteins during cell division and proliferation. May play a regulatory or permissive role in the normal embryonic cardiomyocyte cell cycle and in promoting continued mitosis in transformed, abnormally dividing neonatal cardiomyocytes. Interaction with RB directs embryonic stem cells toward a cardiac lineage. Involved in the regulation of DNA synthesis and hence cell cycle progression, via its C-terminus. Has a potential role regulating skeletal myogenesis and in cell differentiation in embryogenesis. Involved in dendritic cell regulation of T-cell immunity against chlamydia. {ECO:0000269|PubMed:12974617, ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:7542657, ECO:0000269|PubMed:7651420}.; ",{"$nulls":4},"p.Pro2947Ser","c.8839C>T","MODERATE","2947/3114",18,{"$nulls":5},"4","365","197","300","158",null,null,"0","0",{"$nulls":22},"0.644795","4.07",null,"1","-0.98",null,"0.362","0.152",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein that associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. In late G2 the protein associates with the kinetochore and maintains this association through early anaphase. It localizes to the spindle midzone and the intracellular bridge in late anaphase and telophase, respectively, and is thought to be subsequently degraded. The localization of this protein suggests that it may play a role in chromosome segregation during mitotis. It is thought to form either a homodimer or heterodimer. Autoantibodies against this protein have been found in patients with cancer or graft versus host disease. [provided by RefSeq, Jul 2008].  ",null,"C1855705","0/0","365,0","0","365","0/1","160,32","0.1667","192",null,"chr1:214657286:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1582"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CENPF","chr1:214657286","CENPF(P2947S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Stromme syndrome (STROMS) [MIM:243605]: An autosomal recessive congenital disorder characterized by intestinal atresia, ocular anomalies, microcephaly, and renal and cardiac abnormalities in some patients. The disease has features of a ciliopathy, and lethality in early childhood is observed in severe cases. {ECO:0000269|PubMed:25564561, ECO:0000269|PubMed:26820108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for kinetochore function and chromosome segregation in mitosis. Required for kinetochore localization of dynein, LIS1, NDE1 and NDEL1. Regulates recycling of the plasma membrane by acting as a link between recycling vesicles and the microtubule network though its association with STX4 and SNAP25. Acts as a potential inhibitor of pocket protein-mediated cellular processes during development by regulating the activity of RB proteins during cell division and proliferation. May play a regulatory or permissive role in the normal embryonic cardiomyocyte cell cycle and in promoting continued mitosis in transformed, abnormally dividing neonatal cardiomyocytes. Interaction with RB directs embryonic stem cells toward a cardiac lineage. Involved in the regulation of DNA synthesis and hence cell cycle progression, via its C-terminus. Has a potential role regulating skeletal myogenesis and in cell differentiation in embryogenesis. Involved in dendritic cell regulation of T-cell immunity against chlamydia. {ECO:0000269|PubMed:12974617, ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:7542657, ECO:0000269|PubMed:7651420}.; ",{"$nulls":4},"p.Pro2947Ser","c.8839C>T","MODERATE","2947/3114",18,{"$nulls":5},"4","365","224","300","176",null,null,"0","0",{"$nulls":22},"0.644795","4.07",null,"1","-0.98",null,"0.362","0.152",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein that associates with the centromere-kinetochore complex. The protein is a component of the nuclear matrix during the G2 phase of interphase. In late G2 the protein associates with the kinetochore and maintains this association through early anaphase. It localizes to the spindle midzone and the intracellular bridge in late anaphase and telophase, respectively, and is thought to be subsequently degraded. The localization of this protein suggests that it may play a role in chromosome segregation during mitotis. It is thought to form either a homodimer or heterodimer. Autoantibodies against this protein have been found in patients with cancer or graft versus host disease. [provided by RefSeq, Jul 2008].  ",null,"C1855705","0/0","366,0","0","366","0/1","117,96","0.4507","213",null,"chr1:214657286:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4318"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CGN","chr1:151524325","CGN(Q456H)",null,null,"coiled-coil region , compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably plays a role in the formation and regulation of the tight junction (TJ) paracellular permeability barrier.; ",{"$nulls":4},"p.Gln456His","c.1368G>T","MODERATE","456/1203",7,{"$nulls":5},"5","533","332","352","216","504","302","0","0","0","0.1126",{"$nulls":20},"1.709931","-0.17",null,"1","-0.95",null,"0.129","0.23",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","528,0","0","528","0/1","282,43","0.1323","325",null,"chr1:151524325:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1296"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CHD6","chr20:41421747","CHD6(G1627fs)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: DNA-dependent ATPase that plays a role in chromatin remodeling. Regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin (PubMed:28533432). Activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2. {ECO:0000269|PubMed:16314513, ECO:0000269|PubMed:28533432}.; ",{"$nulls":4},"p.Gly1627fs","c.4878_4887delAGGAAATCTC","HIGH","1626/2715",31,{"$nulls":5},"5","925","409","751","321","785","348","0","0","0","0.1379",{"$nulls":5},"(CHD6|ENSG00000124177|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the SNF2/RAD54 helicase protein family. The encoded protein contains two chromodomains, a helicase domain, and an ATPase domain. Several multi-subunit protein complexes remodel chromatin to allow patterns of cell type-specific gene expression, and the encoded protein is thought to be a core member of one or more of these chromatin remodeling complexes. The encoded protein may function as a transcriptional repressor and is involved in the cellular repression of influenza virus replication. [provided by RefSeq, Jul 2013].  ",null,null,"0/0","983,0","0","983","0/1","361,55","0.1322","416",null,"chr20:41421747:AGAGATTTCCT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1402"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CLCN4","chrX:10208510","CLCN4(G437C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against protons. {ECO:0000269|PubMed:23647072, ECO:0000269|PubMed:25644381}.; ",{"$nulls":4},"p.Gly437Cys","c.1309G>T","MODERATE","437/760",9,{"$nulls":5},"4","1174","423","917","321","1051","366","0.0009","0.0009","0","0.2814",{"$nulls":20},"3.83434","-2.55;-2.61;-3.02",".;3.215;.","1","-6.83;-6.98;-7.09",".;0.995;.","0.0;0.001;0.0","0.712;0.718;0.682",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0796221","0/0","1178,1","0.0008","1179","0/1","292,116","0.2843","408",null,"chrX:10208510:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.2804"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CLDN25","chr11:113779875","CLDN25(T27N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium- independent cell-adhesion activity. {ECO:0000250}.; ",{"$nulls":4},"p.Thr27Asn","c.80C>A","MODERATE","27/229",1,{"$nulls":5},"4","838","544","646","413","683","445","0.0012","0.0012","0","0.0809",{"$nulls":20},"2.346403","-2.44","2.79","0.995362","-3.82","0.988","0.003","0.693",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","823,0","0","823","0/1","471,38","0.0747","509",null,"chr11:113779875:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0678"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CLDN25","chr11:113779875","CLDN25(T27N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a major role in tight junction-specific obliteration of the intercellular space, through calcium- independent cell-adhesion activity. {ECO:0000250}.; ",{"$nulls":4},"p.Thr27Asn","c.80C>A","MODERATE","27/229",1,{"$nulls":5},"4","838","414","646","334","682","365","0.0012","0.0012","0","0.3644",{"$nulls":20},"2.346403","-2.44","2.79","0.995362","-3.82","0.988","0.003","0.693",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","831,0","0","831","0/1","272,138","0.3366","410",null,"chr11:113779875:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3413"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CLEC1A","chr12:10071377","CLEC1A(E267Q)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu267Gln","c.799G>C","MODERATE","267/280",6,{"$nulls":5},"5","439","592","372","482","355","484","0","0","0","0.0702",{"$nulls":20},"1.021571","4.91;4.91;4.83","1.585;.;.","1","-1.53;-1.61;-1.5","0.006;0.079;0.307","0.035;0.04;0.028","0.066;0.09;0.081",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C3279774","0/0","424,0","0","424","0/1","521,40","0.0713","561",null,"chr12:10071377:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0747"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CNNM4","chr2:96761586","CNNM4(S196W)",null,null,"transmembrane region (Helical ), domain (CNNM transmembrane ), splice variant (In isoform 2. ), sequence variant (In JALIS. CNNM4(S196P))",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable metal transporter. The interaction with the metal ion chaperone COX11 suggests that it may play a role in sensory neuron functions (By similarity). May play a role in biomineralization and retinal function. {ECO:0000250, ECO:0000269|PubMed:19200525, ECO:0000269|PubMed:19200527}.; ",{"$nulls":4},"p.Ser196Trp","c.587C>G","MODERATE","196/775",1,{"$nulls":5},"4","1295","715","1033","539","1109","623","0","0","0","0.1525",{"$nulls":20},"4.18085","-2.85","4.21","1","-5.73","1.0",null,"0.933",{"$nulls":3},"Unknown",-1,"AR","Jalili syndrome","Dental; Ophthalmologic",{"$nulls":3},"C3495589","0/0","1277,0","0","1277","0/1","579,119","0.1705","698",null,"chr2:96761586:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1688"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","CNOT10","chr3:32716279","CNOT10(L270V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is not required for association of CNOT7 to the CCR4- NOT complex. {ECO:0000269|PubMed:23221646}.; ",{"$nulls":4},"p.Leu270Val","c.808C>G","MODERATE","270/804",6,{"$nulls":5},"5","226","128","147","82","204","114","0","0","0","0.0614",{"$nulls":20},"0.91487","0.94","-0.345;-0.345;.","0.999981;0.999981;0.999981;0.998686","-0.12;-0.12;-0.13","0.001;0.0;.","1.0;1.0;0.989","0.167;0.126;0.124",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","219,0","0","219","0/1","113,9","0.0738","122",null,"chr3:32716279:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0854"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CNOT10","chr3:32716279","CNOT10(L270V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is not required for association of CNOT7 to the CCR4- NOT complex. {ECO:0000269|PubMed:23221646}.; ",{"$nulls":4},"p.Leu270Val","c.808C>G","MODERATE","270/804",6,{"$nulls":5},"5","226","133","147","84","202","122","0","0","0","0.2131",{"$nulls":20},"0.91487","0.94","-0.345;-0.345;.","0.999981;0.999981;0.999981;0.998686","-0.12;-0.12;-0.13","0.001;0.0;.","1.0;1.0;0.989","0.167;0.126;0.124",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","219,0","0","219","0/1","103,25","0.1953","128",null,"chr3:32716279:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2024"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","COL6A5","chr3:130440452","COL6A5(Q2038H)",null,null,"domain (VWFA 9 ), region of interest (Nonhelical region )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.; ","FUNCTION: Collagen VI acts as a cell-binding protein. {ECO:0000250}.; ",{"$nulls":4},"p.Gln2038His","c.6114A>C","MODERATE","2038/2615",35,{"$nulls":5},"5","947","506","777","406","764","413","0","0","0","0.0654",{"$nulls":20},"1.189175",null,null,"1",{"$nulls":3},"0.084",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","942,0","0","942","0/1","469,31","0.062","500",null,"chr3:130440452:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0567"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","COL6A5","chr3:130440452","COL6A5(Q2038H)",null,null,"domain (VWFA 9 ), region of interest (Nonhelical region )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Patients affected by atopic dermatitis display an abnormal distribution of COL29A1 mRNA and protein in skin suggesting that COL29A1 may be involved in the pathogenesis of the disease.; ","FUNCTION: Collagen VI acts as a cell-binding protein. {ECO:0000250}.; ",{"$nulls":4},"p.Gln2038His","c.6114A>C","MODERATE","2038/2615",35,{"$nulls":5},"5","947","455","777","369","769","367","0","0","0","0.2425",{"$nulls":20},"1.189175",null,null,"1",{"$nulls":3},"0.084",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","942,0","0","942","0/1","350,97","0.217","447",null,"chr3:130440452:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2033"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","COMMD1","chr2:62000767","COMMD1(Q83*)",null,null,"region of interest (Sufficient for interaction with SLC12A2 ), strand ",{"$nulls":3},255,"PASS","Loss Of Function","rs946359108",-1,null,"FUNCTION: Proposed scaffold protein that is implicated in diverse physiological processes and whose function may be in part linked to its ability to regulate ubiquitination of specific cellular proteins. Can modulate activity of cullin-RING E3 ubiquitin ligase (CRL) complexes by displacing CAND1; in vitro promotes CRL E3 activity and dissociates CAND1 from CUL1 and CUL2 (PubMed:21778237). Promotes ubiquitination of NF-kappa-B subunit RELA and its subsequent proteasomal degradation. Down-regulates NF-kappa-B activity (PubMed:15799966, PubMed:17183367, PubMed:20048074). Involved in the regulation of membrane expression and ubiquitination of SLC12A2 (PubMed:23515529). Modulates Na(+) transport in epithelial cells by regulation of apical cell surface expression of amiloride-sensitive sodium channel (ENaC) subunits and by promoting their ubiquitination presumably involving NEDD4L. Promotes the localization of SCNN1D to recycling endosomes (PubMed:14645214, PubMed:20237237, PubMed:21741370). Promotes CFTR cell surface expression through regulation of its ubiquitination (PubMed:21483833). Down-regulates SOD1 activity by interfering with its homodimerization (PubMed:20595380). Plays a role in copper ion homeostasis. Involved in copper-dependent ATP7A trafficking between the trans- Golgi network and vesicles in the cell periphery; the function is proposed to depend on its association within the CCC complex and cooperation with the WASH complex on early endosomes (PubMed:25355947). Can bind one copper ion per monomer (PubMed:17309234). May function to facilitate biliary copper excretion within hepatocytes. Binds to phosphatidylinositol 4,5- bisphosphate (PtdIns(4,5)P2) (PubMed:18940794). Involved in the regulation of HIF1A-mediated transcription; competes with ARNT/Hif-1-beta for binding to HIF1A resulting in decreased DNA binding and impaired transcriptional activation by HIF-1 (PubMed:20458141). Negatively regulates neuroblastoma G1/S phase cell cycle progression and cell proliferation by stimulating ubiquitination of NF-kappa-B subunit RELA and NF-kappa-B degradation in a FAM107A- and actin-dependent manner (PubMed:28604741). {ECO:0000269|PubMed:14645214, ECO:0000269|PubMed:14685266, ECO:0000269|PubMed:15799966, ECO:0000269|PubMed:16573520, ECO:0000269|PubMed:17183367, ECO:0000269|PubMed:17309234, ECO:0000269|PubMed:20048074, ECO:0000269|PubMed:20237237, ECO:0000269|PubMed:20458141, ECO:0000269|PubMed:20595380, ECO:0000269|PubMed:21483833, ECO:0000269|PubMed:21741370, ECO:0000269|PubMed:21778237, ECO:0000269|PubMed:23515529, ECO:0000269|PubMed:25355947, ECO:0000269|PubMed:28604741}.; ",{"$nulls":4},"p.Gln83*","c.247C>T","HIGH","83/190",2,1,{"$nulls":4},"5","209","174","169","143","165","146","0","0","0","0.1438",{"$nulls":5},"(COMMD1|ENSG00000173163|1|1.00)","(COMMD1|ENSG00000173163|1|1.00)",{"$nulls":13},"7.072271",null,null,"1",{"$nulls":3},"0.89",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","210,0","0","210","0/1","147,20","0.1198","167",null,"chr2:62000767:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1259"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","COPS7A","chr12:6728229","COPS7A(A82G)",null,null,"domain (PCI )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively. {ECO:0000269|PubMed:11285227, ECO:0000269|PubMed:11337588, ECO:0000269|PubMed:12628923, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:9535219}.; ",{"$nulls":4},"p.Ala82Gly","c.245C>G","MODERATE","82/275",4,{"$nulls":5},"5","519","657","408","488","434","545","0","0","0","0.0661",{"$nulls":20},"2.477248","1.5;1.5;1.5;1.5;.;1.5;1.5;1.5;1.5","1.22;1.22;1.22;.;.;1.22;.;1.22;.","0.982898","-1.66;-1.66;-1.66;-1.63;-1.74;-1.66;-1.63;-1.66;-1.63","0.001;0.001;0.001;0.05;.;0.001;.;0.001;.","0.237;0.237;0.237;0.214;0.25;0.237;0.177;0.237;0.176","0.316;0.316;0.316;0.257;.;0.318;.;0.316;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","512,0","0","512","0/1","580,39","0.063","619",null,"chr12:6728229:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0615"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","CRYBG3","chr3:97876454","CRYBG3(E1754K)",{"$nulls":6},255,"PASS","Missense","rs569798970",0.00226928895612708,null,"FUNCTION: Isoform vlAKAP: Anchoring protein that mediates the subcellular compartmentation of protein kinase A (PKA). {ECO:0000269|PubMed:25097019}.; ",{"$nulls":4},"p.Glu1754Lys","c.5260G>A","MODERATE","1754/2970",4,{"$nulls":5},"5","401","168","326","140","276","130","0","0","0","0.2923",{"$nulls":20},"1.310788",{"$nulls":6},"0.136",{"$nulls":3},"1000Gp3_AFR_AF",0.00226928895612708,{"$nulls":7},"0/0","402,0","0","402","0/1","120,45","0.2727","165",null,"chr3:97876454:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2571"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","DAXX","chr6:33321419","DAXX(R119Q)",null,null,"region of interest (Necessary for interaction with USP7 and ATRX )",{"$nulls":3},255,"PASS","Missense","rs771284147",2.6968716289104636E-4,null,"FUNCTION: Transcription corepressor known to repress transcriptional potential of several sumoylated transcription factors. Down-regulates basal and activated transcription. Its transcription repressor activity is modulated by recruiting it to subnuclear compartments like the nucleolus or PML/POD/ND10 nuclear bodies through interactions with MCSR1 and PML, respectively. Seems to regulate transcription in PML/POD/ND10 nuclear bodies together with PML and may influence TNFRSF6-dependent apoptosis thereby. Inhibits transcriptional activation of PAX3 and ETS1 through direct protein-protein interactions. Modulates PAX5 activity; the function seems to involve CREBBP. Acts as an adapter protein in a MDM2-DAXX-USP7 complex by regulating the RING-finger E3 ligase MDM2 ubiquitination activity. Under non-stress condition, in association with the deubiquitinating USP7, prevents MDM2 self-ubiquitination and enhances the intrinsic E3 ligase activity of MDM2 towards TP53, thereby promoting TP53 ubiquitination and subsequent proteasomal degradation. Upon DNA damage, its association with MDM2 and USP7 is disrupted, resulting in increased MDM2 autoubiquitination and consequently, MDM2 degradation, which leads to TP53 stabilization. Acts as histone chaperone that facilitates deposition of histone H3.3. Acts as targeting component of the chromatin remodeling complex ATRX:DAXX which has ATP-dependent DNA translocase activity and catalyzes the replication-independent deposition of histone H3.3 in pericentric DNA repeats outside S-phase and telomeres, and the in vitro remodeling of H3.3-containing nucleosomes. Does not affect the ATPase activity of ATRX but alleviates its transcription repression activity. Upon neuronal activation associates with regulatory elements of selected immediate early genes where it promotes deposition of histone H3.3 which may be linked to transcriptional induction of these genes. Required for the recruitment of histone H3.3:H4 dimers to PML-nuclear bodies (PML- NBs); the process is independent of ATRX and facilitated by ASF1A; PML-NBs are suggested to function as regulatory sites for the incorporation of newly synthesized histone H3.3 into chromatin. In case of overexpression of centromeric histone variant CENPA (as found in various tumors) is involved in its mislocalization to chromosomes; the ectopic localization involves a heterotypic tetramer containing CENPA, and histones H3.3 and H4 and decreases binding of CTCF to chromatin. Proposed to mediate activation of the JNK pathway and apoptosis via MAP3K5 in response to signaling from TNFRSF6 and TGFBR2. Interaction with HSPB1/HSP27 may prevent interaction with TNFRSF6 and MAP3K5 and block DAXX-mediated apoptosis. In contrast, in lymphoid cells JNC activation and TNFRSF6-mediated apoptosis may not involve DAXX. Shows restriction activity towards human cytomegalovirus (HCMV). Plays a role as a positive regulator of the heat shock transcription factor HSF1 activity during the stress protein response (PubMed:15016915). {ECO:0000269|PubMed:12140263, ECO:0000269|PubMed:14990586, ECO:0000269|PubMed:15016915, ECO:0000269|PubMed:15364927, ECO:0000269|PubMed:16845383, ECO:0000269|PubMed:17081986, ECO:0000269|PubMed:17942542, ECO:0000269|PubMed:20504901, ECO:0000269|PubMed:20651253, ECO:0000269|PubMed:23222847, ECO:0000269|PubMed:24200965, ECO:0000269|PubMed:24530302}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Arg119Gln","c.356G>A","MODERATE","119/740",3,1,{"$nulls":4},"3","941","492","690","365",null,null,"0.0021","0.0021",{"$nulls":22},"2.299467",null,"1.465;1.465;.;1.465;.","0.598853","-0.66;-0.66;-0.76;.;-2.23","0.998;0.998;.;.;.","0.026;0.026;0.016;.;0.036","0.133;0.13;0.13;0.182;.",{"$nulls":3},"TWINSUK_AF",2.6968716289104636E-4,{"$nulls":3},"COSMIC,kMAPK",{"$nulls":3},"0/0","916,2","0.0022","918","0/1","397,68","0.1462","465",null,"chr6:33321419:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1452"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","DCHS1","chr11:6633791","DCHS1(S739L)",null,null,"topological domain (Extracellular ), domain (Cadherin 7 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Mitral valve prolapse 2 (MVP2) [MIM:607829]: A form of mitral valve prolapse, a valvular hearth disease characterized by abnormally elongated and thickened mitral valve leaflets, that typically show myxomatous degeneration with increased leaflet compliance. It is associated with mitral regurgitation. Myxomatous mitral valves have an abnormal layered architecture characterized by loose collagen in fibrosa, expanded spongiosa strongly positive for proteoglycans, and disrupted elastin in atrialis. In classic mitral valve prolapse, leaflets are at least 5 mm thick, whereas in the non-classic form, they are less than 5 mm thick. Severe classic mitral valve prolapse is strongly associated with arrhythmias, endocarditis, heart failure, and need for valve surgery. {ECO:0000269|PubMed:26258302}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium-dependent cell-adhesion protein. Mediates functions in neuroprogenitor cell proliferation and differentiation. In the heart, has a critical role for proper morphogenesis of the mitral valve, acting in the regulation of cell migration involved in valve formation (PubMed:26258302). {ECO:0000269|PubMed:26258302}.; ",{"$nulls":4},"p.Ser739Leu","c.2216C>T","MODERATE","739/3298",4,{"$nulls":5},"5","624","270","527","229","511","228","0","0","0","0.2061",{"$nulls":20},"4.856066","0.59","2.045","0.998296","-3.19","0.994","0.007","0.632",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1843003| C4551950","0/0","614,0","0","614","0/1","207,55","0.2099","262",null,"chr11:6633791:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2009"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","DHX36","chr3:154304935","DHX36(I336V)",null,null,"domain (Helicase ATP-binding ), region of interest (RecA-like domain 1 ), short sequence motif (DEAH box )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Multifunctional ATP-dependent helicase that unwinds G- quadruplex (G4) structures (PubMed:16150737, PubMed:18854321, PubMed:20472641, PubMed:21586581). Plays a role in many biological processes such as genomic integrity, gene expression regulations and as a sensor to initiate antiviral responses (PubMed:14731398, PubMed:18279852, PubMed:21993297, PubMed:22238380, PubMed:25579584). G4 structures correspond to helical structures containing guanine tetrads (By similarity). Binds with high affinity to and unwinds G4 structures that are formed in nucleic acids (G4-ADN and G4-RNA) (PubMed:16150737, PubMed:18842585, PubMed:20472641, PubMed:21586581, PubMed:24369427, PubMed:26195789). Plays a role in genomic integrity (PubMed:22238380). Converts the G4-RNA structure present in telomerase RNA template component (TREC) into a double-stranded RNA to promote P1 helix formation that acts as a template boundary ensuring accurate reverse transcription (PubMed:20472641, PubMed:21149580, PubMed:21846770, PubMed:22238380, PubMed:24151078, PubMed:25579584). Plays a role in transcriptional regulation (PubMed:21586581, PubMed:21993297). Resolves G4-DNA structures in promoters of genes, such as YY1, KIT/c-kit and ALPL and positively regulates their expression (PubMed:21993297). Plays a role in post-transcriptional regulation (PubMed:27940037). Unwinds a G4-RNA structure located in the 3'-UTR polyadenylation site of the pre-mRNA TP53 and stimulates TP53 pre-mRNA 3'-end processing in response to ultraviolet (UV)-induced DNA damage (PubMed:27940037). Binds to the precursor-microRNA-134 (pre-miR- 134) terminal loop and regulates its transport into the synapto- dendritic compartment (By similarity). Involved in the pre-miR- 134-dependent inhibition of target gene expression and the control of dendritic spine size (By similarity). Plays a role in the regulation of cytoplasmic mRNA translation and mRNA stability (PubMed:24369427, PubMed:26489465). Binds to both G4-RNA structures and alternative non-quadruplex-forming sequence within the 3'-UTR of the PITX1 mRNA regulating negatively PITX1 protein expression (PubMed:24369427). Binds to both G4-RNA structure in the 5'-UTR and AU-rich elements (AREs) localized in the 3'-UTR of NKX2-5 mRNA to either stimulate protein translation or induce mRNA decay in an ELAVL1-dependent manner, respectively (PubMed:26489465). Binds also to ARE sequences present in several mRNAs mediating exosome-mediated 3'-5' mRNA degradation (PubMed:14731398, PubMed:18279852). Involved in cytoplasmic urokinase-type plasminogen activator (uPA) mRNA decay (PubMed:14731398). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1 (By similarity). Required for early embryonic development and hematopoiesis. Involved in the regulation of cardioblast differentiation and proliferation during heart development. Involved in spermatogonia differentiation. May play a role in ossification (By similarity). {ECO:0000250|UniProtKB:D4A2Z8, ECO:0000250|UniProtKB:Q05B79, ECO:0000250|UniProtKB:Q8VHK9, ECO:0000269|PubMed:14731398, ECO:0000269|PubMed:16150737, ECO:0000269|PubMed:18279852, ECO:0000269|PubMed:18842585, ECO:0000269|PubMed:18854321, ECO:0000269|PubMed:20472641, ECO:0000269|PubMed:21149580, ECO:0000269|PubMed:21586581, ECO:0000269|PubMed:21846770, ECO:0000269|PubMed:21993297, ECO:0000269|PubMed:22238380, ECO:0000269|PubMed:24151078, ECO:0000269|PubMed:24369427, ECO:0000269|PubMed:25579584, ECO:0000269|PubMed:26195789, ECO:0000269|PubMed:26489465, ECO:0000269|PubMed:27940037}.; ",{"$nulls":4},"p.Ile336Val","c.1006A>G","MODERATE","336/1008",8,{"$nulls":5},"4","439","185","305","123","368","157","0","0","0","0.1465",{"$nulls":20},"2.950345","2.84","-0.34;-0.34;-0.34;.","0.999994","-0.72","0.976;0.984;0.867;.","0.138;0.139;0.139;0.083","0.299;0.332;0.298;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","428,0","0","428","0/1","155,26","0.1436","181",null,"chr3:154304935:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1545"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","DLGAP2","chr8:1549625","DLGAP2(D391G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the molecular organization of synapses and neuronal cell signaling. Could be an adapter protein linking ion channel to the subsynaptic cytoskeleton. May induce enrichment of PSD-95/SAP90 at the plasma membrane.; ",{"$nulls":4},"p.Asp391Gly","c.1172A>G","MODERATE","391/1055",5,{"$nulls":5},"4","1698","983","1332","744","1475","854","0","0","0","0.1393",{"$nulls":20},"4.091972",null,".;2.42;.","0.992418",null,".;0.976;.",null,".;.;0.702",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1658,0","0","1658","0/1","814,132","0.1395","946",null,"chr8:1549625:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1478"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","DUSP27","chr1:167126199","DUSP27(K356N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be required for myofiber maturation. {ECO:0000250|UniProtKB:F1QWM2}.; ",{"$nulls":4},"p.Lys356Asn","c.1068G>T","MODERATE","356/1158",6,{"$nulls":5},"5","293","162","238","124","234","128","0","0","0","0.1016",{"$nulls":20},"1.892574","3.89","2.255","1","-0.75","0.883","0.007","0.131;0.144;0.203",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","295,0","0","295","0/1","141,19","0.1187","160",null,"chr1:167126199:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.121"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ECM1","chr1:150511490","ECM1(E275K)",{"$nulls":6},255,"PASS","Missense","rs369508778",2.3255813953488373E-4,null,"FUNCTION: Involved in endochondral bone formation as negative regulator of bone mineralization. Stimulates the proliferation of endothelial cells and promotes angiogenesis. Inhibits MMP9 proteolytic activity. {ECO:0000269|PubMed:11165938, ECO:0000269|PubMed:11292659, ECO:0000269|PubMed:16512877}.; ",{"$nulls":4},"p.Glu275Lys","c.823G>A","MODERATE","275/567",7,{"$nulls":5},"5","717","450","529","333","611","391","0","0","0","0.1202",{"$nulls":20},"4.152816","-1.23",".;2.28","0.998714;0.998714;1","-3.18","1.0","0.004","0.787;0.748",{"$nulls":3},"ESP6500_EA_AF",2.3255813953488373E-4,"AR","Lipoid proteinosis","Audiologic/Otolaryngologic; Biochemical; Dermatologic; Neurologic; Pulmonary",{"$nulls":3},"C0023795","0/0","702,0","0","702","0/1","376,61","0.1396","437",null,"chr1:150511490:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1411"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","EEF2K","chr16:22264834","EEF2K(N465I)",{"$nulls":6},255,"PASS","Missense","rs1333170038",-1,null,"FUNCTION: Threonine kinase that regulates protein synthesis by controlling the rate of peptide chain elongation. Upon activation by a variety of upstream kinases including AMPK or TRPM7, phosphorylates the elongation factor EEF2 at a single site, renders it unable to bind ribosomes and thus inactive. In turn, the rate of protein synthesis is reduced. {ECO:0000269|PubMed:14709557, ECO:0000269|PubMed:9144159}.; ",{"$nulls":4},"p.Asn465Ile","c.1394A>T","MODERATE","465/725",13,{"$nulls":5},"4","941","560","649","381","811","472","0.0011","0.0011","0","0.0678",{"$nulls":20},"0.68621","3.0","1.24","0.999994","-2.02","0.121","0.062","0.6",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","909,0","0","909","0/1","488,35","0.0669","523",null,"chr16:22264834:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0682"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","EEF2K","chr16:22264834","EEF2K(N465I)",{"$nulls":6},255,"PASS","Missense","rs1333170038",-1,null,"FUNCTION: Threonine kinase that regulates protein synthesis by controlling the rate of peptide chain elongation. Upon activation by a variety of upstream kinases including AMPK or TRPM7, phosphorylates the elongation factor EEF2 at a single site, renders it unable to bind ribosomes and thus inactive. In turn, the rate of protein synthesis is reduced. {ECO:0000269|PubMed:14709557, ECO:0000269|PubMed:9144159}.; ",{"$nulls":4},"p.Asn465Ile","c.1394A>T","MODERATE","465/725",13,{"$nulls":5},"4","941","518","649","362","813","432","0.0011","0.0011","0","0.2569",{"$nulls":20},"0.68621","3.0","1.24","0.999994","-2.02","0.121","0.062","0.6",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","899,0","0","899","0/1","366,126","0.2561","492",null,"chr16:22264834:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.268"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","EIF4A2","chr3:186787522","EIF4A2(D314H)",null,null,"domain (Helicase C-terminal )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon.; ","level2",{"$nulls":3},"p.Asp314His","c.940G>C","MODERATE","314/408",9,1,{"$nulls":4},"5","330","294","250","209","281","244","0","0","0","0.0984",{"$nulls":20},"3.846187","-1.0","1.985;.","1","-5.14","0.015;0.012","0.0","0.721;0.722",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","313,0","0","313","0/1","256,27","0.0954","283",null,"chr3:186787522:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0909"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ESYT2","chr7:158799054","ESYT2(E193*)",null,null,"topological domain (Cytoplasmic ), domain (SMP-LTD ), splice variant (In isoform 5. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport. Plays a role in FGF signaling via its role in the rapid internalization of FGFR1 that has been activated by FGF1 binding; this occurs most likely via the AP-2 complex. {ECO:0000269|PubMed:17360437, ECO:0000269|PubMed:20833364, ECO:0000269|PubMed:23791178, ECO:0000269|PubMed:24847877}.; ",{"$nulls":4},"p.Glu193*","c.577G>T","HIGH","193/921",4,{"$nulls":5},"4","596","638","400","439","537","564","0","0","0","0.0762",{"$nulls":5},"(ESYT2|ENSG00000117868|1|1.00)","(ESYT2|ENSG00000117868|1|1.00)",{"$nulls":13},"8.557538",null,null,"1",{"$nulls":3},"0.482;.;0.493",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","585,0","0","585","0/1","569,47","0.0763","616",null,"chr7:158799054:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0729"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","FAF1","chr1:50788015","FAF1(D118N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Ubiquitin-binding protein (PubMed:19722279). Required for the progression of DNA replication forks by targeting DNA replication licensing factor CDT1 for degradation (PubMed:26842564). Potentiates but cannot initiate FAS-induced apoptosis (By similarity). {ECO:0000250|UniProtKB:P54731, ECO:0000269|PubMed:19722279, ECO:0000269|PubMed:26842564}.; ",{"$nulls":4},"p.Asp118Asn","c.352G>A","MODERATE","118/650",4,{"$nulls":5},"5","562","334","452","257","440","265","0","0","0","0.083",{"$nulls":20},"3.638838",null,"1.335;.","0.999996;0.597254;0.999996","-1.8;.","0.986;.","0.235;.","0.594;0.625",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Interaction of Fas ligand (TNFSF6) with the FAS antigen (TNFRSF6) mediates programmed cell death, also called apoptosis, in a number of organ systems. The protein encoded by this gene binds to FAS antigen and can initiate apoptosis or enhance apoptosis initiated through FAS antigen. Initiation of apoptosis by the protein encoded by this gene requires a ubiquitin-like domain but not the FAS-binding domain. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","541,0","0","541","0/1","303,23","0.0706","326",null,"chr1:50788015:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0584"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FAF1","chr1:50788015","FAF1(D118N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Ubiquitin-binding protein (PubMed:19722279). Required for the progression of DNA replication forks by targeting DNA replication licensing factor CDT1 for degradation (PubMed:26842564). Potentiates but cannot initiate FAS-induced apoptosis (By similarity). {ECO:0000250|UniProtKB:P54731, ECO:0000269|PubMed:19722279, ECO:0000269|PubMed:26842564}.; ",{"$nulls":4},"p.Asp118Asn","c.352G>A","MODERATE","118/650",4,{"$nulls":5},"5","562","366","452","286","442","284","0","0","0","0.1831",{"$nulls":20},"3.638838",null,"1.335;.","0.999996;0.597254;0.999996","-1.8;.","0.986;.","0.235;.","0.594;0.625",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Interaction of Fas ligand (TNFSF6) with the FAS antigen (TNFRSF6) mediates programmed cell death, also called apoptosis, in a number of organ systems. The protein encoded by this gene binds to FAS antigen and can initiate apoptosis or enhance apoptosis initiated through FAS antigen. Initiation of apoptosis by the protein encoded by this gene requires a ubiquitin-like domain but not the FAS-binding domain. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","544,0","0","544","0/1","290,60","0.1714","350",null,"chr1:50788015:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1538"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FAM150B","chr2:286125","FAM150B(A129E)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala129Glu","c.386C>A","MODERATE","129/152",4,{"$nulls":5},"5","60","35","61","34","45","23","0","0","0","0.2609",{"$nulls":20},"4.471639",null,null,"0.998064","-4.33;-4.61;-4.61;.;-4.61;-4.29","0.985;.;.;.;.;.","0.004;0.003;0.004;.;0.004;0.004","0.493;0.379;0.351;0.492;0.587;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","61,0","0","61","0/1","28,7","0.2","35",null,"chr2:286125:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1765"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","FAM196B","chr5:169883127","FAM196B(C258R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Cys258Arg","c.772T>C","MODERATE","258/535",2,{"$nulls":5},"4","1049","573","835","446","918","486","0","0","0","0.0947",{"$nulls":20},"3.12132","0.7",null,"0.995213;0.995213;0.995213;0.977619","-0.6","0.739","0.003","0.25",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1032,0","0","1032","0/1","502,52","0.0939","554",null,"chr5:169883127:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1031"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FAM196B","chr5:169883127","FAM196B(C258R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Cys258Arg","c.772T>C","MODERATE","258/535",2,{"$nulls":5},"4","1049","439","835","347","916","386","0","0","0","0.3912",{"$nulls":20},"3.12132","0.7",null,"0.995213;0.995213;0.995213;0.977619","-0.6","0.739","0.003","0.25",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1028,0","0","1028","0/1","261,174","0.4","435",null,"chr5:169883127:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4092"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FAM212B","chr1:111727698","FAM212B(Q41_Q54del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Gln41_Gln54del","c.122_163delAAGAACTGAAGCTCCTCCAGGTGCAGACAGCACTGGAACAGC","MODERATE","41/297",2,{"$nulls":5},"5","719","361","520","266","488","264","0","0","0","0.1629",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","822,0","0","822","0/1","365,50","0.1205","415",null,"chr1:111727698:AGCTGTTCCAGTGCTGTCTGCACCTGGAGGAGCTTCAGTTCTT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1203"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FBN2","chr5:128349473","FBN2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Macular degeneration, early-onset (EOMD) [MIM:616118]: An ocular disorder characterized by macular changes resulting in progressive loss of visual acuity. {ECO:0000269|PubMed:24899048}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Fibrillin-2: Fibrillins are structural components of 10- 12 nm extracellular calcium-binding microfibrils, which occur either in association with elastin or in elastin-free bundles. Fibrillin-2-containing microfibrils regulate the early process of elastic fiber assembly. Regulates osteoblast maturation by controlling TGF-beta bioavailability and calibrating TGF-beta and BMP levels, respectively. {ECO:0000250|UniProtKB:Q61555}.; ",{"$nulls":5},"c.2864-1G>T","HIGH",null,22,{"$nulls":5},"4","343","143","247","100","320","139","0.0029","0.0029","0","0.1799",{"$nulls":5},"(FBN2|ENSG00000138829|1|1.00)",{"$nulls":14},"5.537705",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Congenital contractural arachnodactyly (Beals syndrome)","Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Ophthalmologic",{"$nulls":3},"C0220668| C4015286","0/0","337,1","0.003","338","0/1","116,25","0.1773","141",null,"chr5:128349473:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.16"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","FGF23","chr12:4370509","FGF23(A197fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Hypophosphatemic rickets, autosomal dominant (ADHR) [MIM:193100]: A disease characterized by isolated renal phosphate wasting, hypophosphatemia, and inappropriately normal 1,25- dihydroxyvitamin D3 (calcitriol) levels. Patients frequently present with bone pain, rickets, and tooth abscesses. {ECO:0000269|PubMed:11062477, ECO:0000269|PubMed:11409890, ECO:0000269|PubMed:16638743}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tumoral calcinosis, hyperphosphatemic, familial, 2 (HFTC2) [MIM:617993]: A form of hyperphosphatemic tumoral calcinosis, a rare autosomal recessive metabolic disorder that manifests with hyperphosphatemia and massive calcium deposits in the skin and subcutaneous tissues. Some patients have recurrent, transient, painful swellings of the long bones associated with the radiographic findings of periosteal reaction and cortical hyperostosis and absence of skin involvement. {ECO:0000269|PubMed:15590700, ECO:0000269|PubMed:16030159, ECO:0000269|PubMed:16151858, ECO:0000269|PubMed:24680727}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Regulator of phosphate homeostasis. Inhibits renal tubular phosphate transport by reducing SLC34A1 levels. Upregulates EGR1 expression in the presence of KL (By similarity). Acts directly on the parathyroid to decrease PTH secretion (By similarity). Regulator of vitamin-D metabolism. Negatively regulates osteoblast differentiation and matrix mineralization. {ECO:0000250, ECO:0000269|PubMed:11062477, ECO:0000269|PubMed:11409890, ECO:0000269|PubMed:15040831, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:18282132}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Ala197fs","c.589delG","HIGH","197/251",3,{"$nulls":5},"5","715","563","593","463","557","442","0","0","0","0.1629",{"$nulls":5},"(FGF23|ENSG00000118972|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Hypophosphatemic rickets, autosomal dominant; Tumoral calcinosis, hyperphosphatemic","Dental; Renal; Musculoskeletal","kCANCER,kMAPK",null,null,"C4693863| C0342642","0/0","681,0","0","681","0/1","430,96","0.1825","526",null,"chr12:4370509:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1641"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FGF23","chr12:4370509","FGF23(A197fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Hypophosphatemic rickets, autosomal dominant (ADHR) [MIM:193100]: A disease characterized by isolated renal phosphate wasting, hypophosphatemia, and inappropriately normal 1,25- dihydroxyvitamin D3 (calcitriol) levels. Patients frequently present with bone pain, rickets, and tooth abscesses. {ECO:0000269|PubMed:11062477, ECO:0000269|PubMed:11409890, ECO:0000269|PubMed:16638743}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tumoral calcinosis, hyperphosphatemic, familial, 2 (HFTC2) [MIM:617993]: A form of hyperphosphatemic tumoral calcinosis, a rare autosomal recessive metabolic disorder that manifests with hyperphosphatemia and massive calcium deposits in the skin and subcutaneous tissues. Some patients have recurrent, transient, painful swellings of the long bones associated with the radiographic findings of periosteal reaction and cortical hyperostosis and absence of skin involvement. {ECO:0000269|PubMed:15590700, ECO:0000269|PubMed:16030159, ECO:0000269|PubMed:16151858, ECO:0000269|PubMed:24680727}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Regulator of phosphate homeostasis. Inhibits renal tubular phosphate transport by reducing SLC34A1 levels. Upregulates EGR1 expression in the presence of KL (By similarity). Acts directly on the parathyroid to decrease PTH secretion (By similarity). Regulator of vitamin-D metabolism. Negatively regulates osteoblast differentiation and matrix mineralization. {ECO:0000250, ECO:0000269|PubMed:11062477, ECO:0000269|PubMed:11409890, ECO:0000269|PubMed:15040831, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:18282132}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Ala197fs","c.589delG","HIGH","197/251",3,{"$nulls":5},"4","715","855","593","714","558","736","0","0","0","0.3872",{"$nulls":5},"(FGF23|ENSG00000118972|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Hypophosphatemic rickets, autosomal dominant; Tumoral calcinosis, hyperphosphatemic","Dental; Renal; Musculoskeletal","kCANCER,kMAPK",null,null,"C4693863| C0342642","0/0","679,0","0","679","0/1","479,331","0.4086","810",null,"chr12:4370509:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4076"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FLG","chr1:152309486","FLG(S1800R)",{"$nulls":6},255,"PASS","Missense","rs772604170",-1,"DISEASE: Ichthyosis vulgaris (VI) [MIM:146700]: The most common form of ichthyosis inherited as an autosomal dominant trait. It is characterized by palmar hyperlinearity, keratosis pilaris and a fine scale that is most prominent over the lower abdomen, arms, and legs. Ichthyosis vulgaris is characterized histologically by absent or reduced keratohyalin granules in the epidermis and mild hyperkeratosis. The disease can be associated with frequent asthma, eczema or hay fever. {ECO:0000269|PubMed:16444271}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dermatitis atopic 2 (ATOD2) [MIM:605803]: Atopic dermatitis is a complex, inflammatory disease with multiple alleles at several loci thought to be involved in the pathogenesis. It commonly begins in infancy or early childhood and is characterized by a chronic relapsing form of skin inflammation, a disturbance of epidermal barrier function that culminates in dry skin, and IgE-mediated sensitization to food and environmental allergens. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee. {ECO:0000269|PubMed:16550169, ECO:0000269|PubMed:16815158, ECO:0000269|PubMed:17030239, ECO:0000269|PubMed:17291859}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Aggregates keratin intermediate filaments and promotes disulfide-bond formation among the intermediate filaments during terminal differentiation of mammalian epidermis.; ","gedi",{"$nulls":3},"p.Ser1800Arg","c.5400C>A","MODERATE","1800/4061",3,{"$nulls":5},"4","2244","1383","1823","1070","1810","1080","0","0","0","0.1269",{"$nulls":20},"0.444357","3.82","2.115","1","-1.83","0.963","0.004","0.086",{"$nulls":3},"Unknown",-1,"AD/AR","Icthyosis vulgaris","Dermatologic",{"$nulls":3},"C0079584| C1853965","0/0","2152,0","0","2152","0/1","1128,176","0.135","1304",null,"chr1:152309486:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1252"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","FNDC1","chr6:159232215","FNDC1(P568L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be an activator of G protein signaling. {ECO:0000250}.; ",{"$nulls":4},"p.Pro568Leu","c.1703C>T","MODERATE","568/1894",11,{"$nulls":5},"4","746","455","600","345","585","356","0.0013","0.0013","0","0.059",{"$nulls":20},"0.574216","3.12","0.065","0.999999","-2.71","0.066","0.367","0.059",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","740,1","0.0013","741","0/1","416,27","0.0609","443",null,"chr6:159232215:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.058"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FNDC1","chr6:159232215","FNDC1(P568L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be an activator of G protein signaling. {ECO:0000250}.; ",{"$nulls":4},"p.Pro568Leu","c.1703C>T","MODERATE","568/1894",11,{"$nulls":5},"4","746","411","600","315","585","337","0.0013","0.0013","0","0.2018",{"$nulls":20},"0.574216","3.12","0.065","0.999999","-2.71","0.066","0.367","0.059",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","736,1","0.0014","737","0/1","327,77","0.1906","404",null,"chr6:159232215:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1841"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","FOXC1","chr6:1611055","FOXC1(P205fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Axenfeld-Rieger syndrome 3 (RIEG3) [MIM:602482]: An autosomal dominant disorder of morphogenesis that results in abnormal development of the anterior segment of the eye, and results in blindness from glaucoma in approximately 50% of affected individuals. Features include posterior corneal embryotoxon, prominent Schwalbe line and iris adhesion to the Schwalbe line, hypertelorism, hypodontia, sensorineural deafness, redundant periumbilical skin, and cardiovascular defects such as patent ductus arteriosus and atrial septal defect. When associated with tooth anomalies, the disorder is known as Rieger syndrome. {ECO:0000269|PubMed:11170889, ECO:0000269|PubMed:11179011, ECO:0000269|PubMed:11589884, ECO:0000269|PubMed:11740218, ECO:0000269|PubMed:12454026, ECO:0000269|PubMed:12592227, ECO:0000269|PubMed:14506133, ECO:0000269|PubMed:14578375, ECO:0000269|PubMed:15277473, ECO:0000269|PubMed:15477465, ECO:0000269|PubMed:16449236, ECO:0000269|PubMed:16936096, ECO:0000269|PubMed:17210863, ECO:0000269|PubMed:17653043, ECO:0000269|PubMed:19279310, ECO:0000269|PubMed:23239455, ECO:0000269|PubMed:24914578, ECO:0000269|PubMed:25786029, ECO:0000269|PubMed:27804176, ECO:0000269|PubMed:9792859}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Anterior segment dysgenesis 3 (ASGD3) [MIM:601631]: A form of anterior segment dysgenesis, a group of defects affecting anterior structures of the eye including cornea, iris, lens, trabecular meshwork, and Schlemm canal. Anterior segment dysgeneses result from abnormal migration or differentiation of the neural crest derived mesenchymal cells that give rise to components of the anterior chamber during eye development. Different anterior segment anomalies may exist alone or in combination, including iris hypoplasia, enlarged or reduced corneal diameter, corneal vascularization and opacity, posterior embryotoxon, corectopia, polycoria, abnormal iridocorneal angle, ectopia lentis, and anterior synechiae between the iris and posterior corneal surface. Clinical conditions falling within the phenotypic spectrum of anterior segment dysgeneses include aniridia, Axenfeld anomaly, Reiger anomaly/syndrome, Peters anomaly, and iridogoniodysgenesis. ASGD3 inheritance is autosomal dominant. {ECO:0000269|PubMed:12614756, ECO:0000269|PubMed:18484311, ECO:0000269|PubMed:19279310, ECO:0000269|PubMed:19793056, ECO:0000269|PubMed:20881294, ECO:0000269|PubMed:9620769}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: DNA-binding transcriptional factor that plays a role in a broad range of cellular and developmental processes such as eye, bones, cardiovascular, kidney and skin development (PubMed:11782474, PubMed:15299087, PubMed:15684392, PubMed:16492674, PubMed:27907090, PubMed:14506133, PubMed:14578375, PubMed:15277473, PubMed:16449236, PubMed:17210863, PubMed:19793056, PubMed:19279310, PubMed:25786029, PubMed:27804176). Acts either as a transcriptional activator or repressor (PubMed:11782474). Binds to the consensus binding site 5'-[G/C][A/T]AAA[T/C]AA[A/C]-3' in promoter of target genes (PubMed:7957066, PubMed:11782474, PubMed:12533514, PubMed:14506133, PubMed:19793056, PubMed:27804176). Upon DNA-binding, promotes DNA bending (PubMed:7957066, PubMed:14506133). Acts as a transcriptional coactivator (PubMed:26565916). Stimulates Indian hedgehog (Ihh)- induced target gene expression mediated by the transcription factor GLI2, and hence regulates endochondral ossification (By similarity). Acts also as a transcriptional coregulator by increasing DNA-binding capacity of GLI2 in breast cancer cells (PubMed:26565916). Regulates FOXO1 through binding to a conserved element, 5'-GTAAACAAA-3' in its promoter region, implicating FOXC1 as an important regulator of cell viability and resistance to oxidative stress in the eye (PubMed:17993506). Cooperates with transcription factor FOXC2 in regulating expression of genes that maintain podocyte integrity (By similarity). Promotes cell growth inhibition by stopping the cell cycle in the G1 phase through TGFB1-mediated signals (PubMed:12408963). Involved in epithelial- mesenchymal transition (EMT) induction by increasing cell proliferation, migration and invasion (PubMed:20406990, PubMed:22991501). Involved in chemokine CXCL12-induced endothelial cell migration through the control of CXCR4 expression (By similarity). Plays a role in the gene regulatory network essential for epidermal keratinocyte terminal differentiation (PubMed:27907090). Essential developmental transcriptional factor required for mesoderm-derived tissues, such as the somites, skin, bone and cartilage. Positively regulates CXCL12 and stem cell factor expression in bone marrow mesenchymal progenitor cells, and hence plays a role in the development and maintenance of mesenchymal niches for haematopoietic stem and progenitor cells (HSPC). Plays a role in corneal transparency by preventing both blood vessel and lymphatic vessel growth during embryonic development in a VEGF-dependent manner. Involved in chemokine CXCL12-induced endothelial cell migration through the control of CXCR4 expression (By similarity). May function as a tumor suppressor (PubMed:12408963). {ECO:0000250|UniProtKB:Q61572, ECO:0000269|PubMed:11782474, ECO:0000269|PubMed:12408963, ECO:0000269|PubMed:12533514, ECO:0000269|PubMed:14506133, ECO:0000269|PubMed:14578375, ECO:0000269|PubMed:15277473, ECO:0000269|PubMed:15299087, ECO:0000269|PubMed:15684392, ECO:0000269|PubMed:16449236, ECO:0000269|PubMed:16492674, ECO:0000269|PubMed:17210863, ECO:0000269|PubMed:17993506, ECO:0000269|PubMed:19279310, ECO:0000269|PubMed:19793056, ECO:0000269|PubMed:20406990, ECO:0000269|PubMed:22991501, ECO:0000269|PubMed:25786029, ECO:0000269|PubMed:26565916, ECO:0000269|PubMed:27804176, ECO:0000269|PubMed:27907090, ECO:0000269|PubMed:7957066}.; ",{"$nulls":4},"p.Pro205fs","c.613_631delCCGCCGGAGCAGGCCGACG","HIGH","205/553",1,{"$nulls":5},"5","697","311","577","231","669","290","0","0","0","0.1724",{"$nulls":5},"(FOXC1|ENSG00000054598|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Peters anomaly; Axenfeld-Rieger syndrome, type 3; Iridogoiodysgenesis, type 1","Audiologic/Otolaryngologic; Cardiovascular; Musculoskeletal; Ophthalmologic",{"$nulls":3},"C1866560| C2678503","0/0","871,0","0","871","0/1","302,58","0.1611","360",null,"chr6:1611055:GCGCCGCCGGAGCAGGCCGA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1472"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GAB4","chr22:16970189","GAB4(A231P)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala231Pro","c.691G>C","MODERATE","231/574",4,{"$nulls":5},"5","313","135","227","101","293","121","0","0","0","0.2314",{"$nulls":20},"3.458363","1.08;.","2.135;.","0.999785","-1.81;.","1.0;.","0.003;.","0.398;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","314,0","0","314","0/1","100,34","0.2537","134",null,"chr22:16970189:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.2574"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GLB1L3","chr11:134281397","GLB1L3(H128L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.His128Leu","c.383A>T","MODERATE","128/653",4,{"$nulls":5},"4","1699","852","1267","610","1498","701","0","0","0","0.1084",{"$nulls":20},"3.437896","-4.64","2.73","0.999998","-10.57;-9.92","1.0;0.999","0.001;0.0","0.922;0.92",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1637,0","0","1637","0/1","706,84","0.1063","790",null,"chr11:134281397:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1082"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GPR22","chr7:107474651","GPR22(C197W)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Orphan G-protein coupled receptor. Seems to act through a G(i)/G(o) mediated pathway (PubMed:18539757). May be involved in ciliogenesis (By similarity). {ECO:0000250|UniProtKB:A0A2R9YJI3, ECO:0000269|PubMed:18539757}.; ",{"$nulls":4},"p.Cys197Trp","c.591T>G","MODERATE","197/433",3,{"$nulls":5},"4","414","247","348","214","351","199","0","0","0","0.1658",{"$nulls":20},"3.004263","0.01","1.2","1","-2.84","0.951","0.003","0.882",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","412,1","0.0024","413","0/1","208,40","0.1613","248",null,"chr7:107474651:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1542"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GPT2","chr16:46926956","GPT2(C467Y)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the reversible transamination between alanine and 2-oxoglutarate to form pyruvate and glutamate. {ECO:0000269|PubMed:11863375}.; ","mitocarta",{"$nulls":3},"p.Cys467Tyr","c.1400G>A","MODERATE","467/523",11,{"$nulls":5},"4","1092","602","801","435","931","514","0","0","0","0.177",{"$nulls":20},"4.305198","2.03;2.0","3.735;.","1","-6.43;-6.32","1.0;0.999","0.0","0.906;0.907",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225388","0/0","1072,0","0","1072","0/1","480,93","0.1623","573",null,"chr16:46926956:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1701"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GRM3","chr7:86786979","GRM3(A396V)",null,null,"topological domain (Extracellular ), disulfide bond , helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: G-protein coupled receptor for glutamate. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Signaling inhibits adenylate cyclase activity. {ECO:0000269|PubMed:8840013}.; ",{"$nulls":4},"p.Ala396Val","c.1187C>T","MODERATE","396/879",3,1,{"$nulls":4},"4","876","511","676","385","750","445","0","0","0","0.1685",{"$nulls":20},"3.657966","-3.44","4.22","1","-3.54;-3.6","1.0;.","0.0","0.952;0.95",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","856,0","0","856","0/1","414,75","0.1534","489",null,"chr7:86786979:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1636"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GUCY2C","chr12:14656533","GUCY2C(E483D)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Diarrhea 6 (DIAR6) [MIM:614616]: A relatively mild, early-onset chronic diarrhea that may be associated with increased susceptibility to inflammatory bowel disease, small bowel obstruction, and esophagitis. {ECO:0000269|PubMed:22436048}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Meconium ileus (MECIL) [MIM:614665]: A condition characterized by a intestinal obstruction due to inspissated meconium in the distal ileum and cecum, which develops in utero and presents shortly after birth as a failure to pass meconium. Meconium ileus is a known clinical manifestation of cystic fibrosis. {ECO:0000269|PubMed:22521417}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor for the E.coli heat-stable enterotoxin (E.coli enterotoxin markedly stimulates the accumulation of cGMP in mammalian cells expressing GC-C). Also activated by the endogenous peptides guanylin and uroguanylin.; ",{"$nulls":4},"p.Glu483Asp","c.1449G>C","MODERATE","483/1073",12,{"$nulls":5},"5","552","412","432","311","482","356","0","0","0","0.1517",{"$nulls":20},"2.271978","-1.55","2.32","0.999871","-0.91","0.357","0.252","0.286",{"$nulls":3},"Unknown",-1,"AD/AR","Diarrhea 6; Meconium ileus","Gastrointestinal; Renal",{"$nulls":3},"C3553270| C2939175","0/0","545,0","0","545","0/1","337,58","0.1468","395",null,"chr12:14656533:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1511"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","GYS1","chr19:48969428","GYS1(E692Q)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Muscle glycogen storage disease 0 (GSD0b) [MIM:611556]: Metabolic disorder characterized by fasting hypoglycemia presenting in infancy or early childhood. The role of muscle glycogen is to provide critical energy during bursts of activity and sustained muscle work. {ECO:0000269|PubMed:17928598}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan.; ",{"$nulls":4},"p.Glu692Gln","c.2074G>C","MODERATE","692/737",16,{"$nulls":5},"5","704","432","531","303","606","369","0","0","0","0.0542",{"$nulls":20},"1.9253149999999999","-0.08;-0.36","1.39;.","0.740539;0.740539;0.740539;0.519825","-0.28;-0.31","0.028;.","0.105;0.084","0.14;0.15",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease, type 0, muscle","Biochemical; Cardiovascular; Musculoskeletal; Neurologic",{"$nulls":3},"C1969054","0/0","698,0","0","698","0/1","407,24","0.0557","431",null,"chr19:48969428:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0561"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","GYS1","chr19:48969428","GYS1(E692Q)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Muscle glycogen storage disease 0 (GSD0b) [MIM:611556]: Metabolic disorder characterized by fasting hypoglycemia presenting in infancy or early childhood. The role of muscle glycogen is to provide critical energy during bursts of activity and sustained muscle work. {ECO:0000269|PubMed:17928598}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan.; ",{"$nulls":4},"p.Glu692Gln","c.2074G>C","MODERATE","692/737",16,{"$nulls":5},"5","704","297","531","224","605","246","0","0","0","0.1748",{"$nulls":20},"1.9253149999999999","-0.08;-0.36","1.39;.","0.740539;0.740539;0.740539;0.519825","-0.28;-0.31","0.028;.","0.105;0.084","0.14;0.15",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease, type 0, muscle","Biochemical; Cardiovascular; Musculoskeletal; Neurologic",{"$nulls":3},"C1969054","0/0","698,0","0","698","0/1","242,52","0.1769","294",null,"chr19:48969428:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1741"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","HCLS1","chr3:121632536","HCLS1(P346A)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate of the antigen receptor-coupled tyrosine kinase. Plays a role in antigen receptor signaling for both clonal expansion and deletion in lymphoid cells. May also be involved in the regulation of gene expression.; ",{"$nulls":4},"p.Pro346Ala","c.1036C>G","MODERATE","346/486",12,{"$nulls":5},"5","375","165","266","114","295","121","0.0027","0.0027","0","0.2231",{"$nulls":20},"3.540899","1.99;1.98","2.38;.","0.999996","-1.97;-1.8","1.0;0.999","0.119;0.13","0.343;0.358",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","370,0","0","370","0/1","125,36","0.2236","161",null,"chr3:121632536:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2193"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","HEATR5A","chr14:31295936","HEATR5A(F1863fs)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Phe1863fs","c.5587_5591delTTTAA","HIGH","1863/2046",34,{"$nulls":5},"5","612","407","451","296","572","380","0","0","0","0.1263",{"$nulls":5},"(HEATR5A|ENSG00000129493|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","619,0","0","619","0/1","332,47","0.124","379",null,"chr14:31295936:TTTAAA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1284"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","HEATR5B","chr2:36981571","HEATR5B(S2045R)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser2045Arg","c.6135C>G","MODERATE","2045/2071",36,{"$nulls":5},"5","902","529","645","360","804","454","0","0","0","0.1432",{"$nulls":20},"1.7822019999999998","0.86","2.14","0.999999;0.965478","-2.15","0.672","0.217","0.395",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","882,0","0","882","0/1","421,79","0.158","500",null,"chr2:36981571:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.15"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","HES6","chr2:238238815","HES6(A198_Ter225delins???)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 4. )","short-sequence-motif:WRPW_motif","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Does not bind DNA itself but suppresses both HES1- mediated N box-dependent transcriptional repression and binding of HES1 to E box sequences. Also suppresses HES1-mediated inhibition of the heterodimer formed by ASCL1/MASH1 and TCF3/E47, allowing ASCL1 and TCF3 to up-regulate transcription in its presence. Promotes cell differentiation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala198_Ter225delins???","c.594_*11delTGAGGGGCCCGACTTGGTGCCCGCAGCCCTGGGCAGCCTGACCACAGCCCAAATTGCCCGGAGTGTCTGGAGGCCTTGGTGACCAATGCCAGC","HIGH","198/224",4,{"$nulls":20},"238238908",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr2:238238815:GGCTGGCATTGGTCACCAAGGCCTCCAGACACTCCGGGCAATTTGGGCTGTGGTCAGGCTGCCCAGGGCTGCGGGCACCAAGTCGGGCCCCTCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","HOXD8","chr2:176130838","HOXD8(Q158K)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.; ",{"$nulls":4},"p.Gln158Lys","c.472C>A","MODERATE","158/290",1,{"$nulls":5},"4","969","606","746","469","740","493","0.0021","0.0021","0","0.1075",{"$nulls":20},"3.891277","0.86;.;0.86","2.66;.;2.66","0.999558;0.999558;0.999558;0.999558;1","-2.94;.;-2.92","0.945;.;.","0.023;.;0.035","0.427;0.496;0.565",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","945,1","0.0011","946","0/1","521,57","0.0986","578",null,"chr2:176130838:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1002"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","HOXD8","chr2:176130838","HOXD8(Q158K)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.; ",{"$nulls":4},"p.Gln158Lys","c.472C>A","MODERATE","158/290",1,{"$nulls":5},"4","969","580","746","447","740","458","0.0021","0.0021","0","0.2467",{"$nulls":20},"3.891277","0.86;.;0.86","2.66;.;2.66","0.999558;0.999558;0.999558;0.999558;1","-2.94;.;-2.92","0.945;.;.","0.023;.;0.035","0.427;0.496;0.565",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","944,1","0.0011","945","0/1","418,128","0.2344","546",null,"chr2:176130838:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2394"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","HSP90AA1","chr14:102084423","HSP90AA1(E497Q)",null,null,"region of interest (Interaction with NR3C1 ), region of interest (Interaction with FLCN and FNIP1 ), region of interest (Interaction with FNIP2 and TSC1 )",{"$nulls":3},255,"PASS","Missense","rs1351357127",-1,null,"FUNCTION: Molecular chaperone that promotes the maturation, structural maintenance and proper regulation of specific target proteins involved for instance in cell cycle control and signal transduction. Undergoes a functional cycle that is linked to its ATPase activity which is essential for its chaperone activity. This cycle probably induces conformational changes in the client proteins, thereby causing their activation. Interacts dynamically with various co-chaperones that modulate its substrate recognition, ATPase cycle and chaperone function (PubMed:11274138, PubMed:15577939, PubMed:15937123, PubMed:27353360, PubMed:29127155). Engages with a range of client protein classes via its interaction with various co-chaperone proteins or complexes, that act as adapters, simultaneously able to interact with the specific client and the central chaperone itself (PubMed:29127155). Recruitment of ATP and co-chaperone followed by client protein forms a functional chaperone. After the completion of the chaperoning process, properly folded client protein and co- chaperone leave HSP90 in an ADP-bound partially open conformation and finally, ADP is released from HSP90 which acquires an open conformation for the next cycle (PubMed:27295069, PubMed:26991466). Apart from its chaperone activity, it also plays a role in the regulation of the transcription machinery. HSP90 and its co-chaperones modulate transcription at least at three different levels (PubMed:25973397). In the first place, they alter the steady-state levels of certain transcription factors in response to various physiological cues(PubMed:25973397). Second, they modulate the activity of certain epigenetic modifiers, such as histone deacetylases or DNA methyl transferases, and thereby respond to the change in the environment (PubMed:25973397). Third, they participate in the eviction of histones from the promoter region of certain genes and thereby turn on gene expression (PubMed:25973397). Binds bacterial lipopolysaccharide (LPS) and mediates LPS-induced inflammatory response, including TNF secretion by monocytes (PubMed:11276205). Antagonizes STUB1- mediated inhibition of TGF-beta signaling via inhibition of STUB1- mediated SMAD3 ubiquitination and degradation (PubMed:24613385). {ECO:0000269|PubMed:11274138, ECO:0000269|PubMed:11276205, ECO:0000269|PubMed:15577939, ECO:0000269|PubMed:15937123, ECO:0000269|PubMed:24613385, ECO:0000269|PubMed:27353360, ECO:0000269|PubMed:29127155, ECO:0000303|PubMed:25973397, ECO:0000303|PubMed:26991466, ECO:0000303|PubMed:27295069}.; ","level2",{"$nulls":3},"p.Glu497Gln","c.1489G>C","MODERATE","497/854",7,{"$nulls":5},"5","586","292","454","233","501","233","0","0","0","0.1502",{"$nulls":20},"3.857571","2.78","2.94;.","1","-2.02;-2.35","0.643;0.927","0.019;0.015","0.379;0.402",{"$nulls":3},"Unknown",-1,{"$nulls":3},"dcPGX,kCANCER",{"$nulls":3},"0/0","579,0","0","579","0/1","241,41","0.1454","282",null,"chr14:102084423:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1545"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","IL21R","chr16:27448813","IL21R(D383H)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Immunodeficiency 56 (IMD56) [MIM:615207]: An autosomal recessive primary immunodeficiency characterized by B- and T-cell defects and variable dysfunction of NK cells. Patients tend to have normal numbers of lymphocytes, but show defective class- switched B-cells, low IgG, defective antibody response, and defective T-cell responses to certain antigens. {ECO:0000269|PubMed:23440042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Chromosomal aberrations involving IL21R is a cause of B-cell non-Hodgkin lymphomas (B-cell NHL). Translocation t(3;16)(q27;p11), with BCL6.; ","FUNCTION: This is a receptor for interleukin-21.; ","gedi|level2",{"$nulls":3},"p.Asp383His","c.1147G>C","MODERATE","383/538",9,{"$nulls":5},"5","1751","818","1305","607","1518","704","0","0","0","0.1918",{"$nulls":20},"2.933472","0.97","2.095","1","-1.85","1.0","0.0","0.236;0.248;0.227",{"$nulls":3},"Unknown",-1,"AR","Immunodeficiency, primary, autosomal recessive, IL21R-related","Allergy/Immunology/Infectious","COSMIC,kJAK_STAT",null,null,"C1840253| C3554687","0/0","1704,0","0","1704","0/1","648,150","0.188","798",null,"chr16:27448813:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1779"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","IQCD","chr12:113207761","IQCD(L136V)",null,null,"sequence variant (In dbSNP:rs7966313. IQCD(L136V))",{"$nulls":3},255,"PASS","Missense","rs7966313",0.01664145234493192,null,"FUNCTION: Component of the nexin-dynein regulatory complex (N- DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. {ECO:0000250|UniProtKB:A8J0N6}.; ",{"$nulls":4},"p.Leu136Val","c.406C>G","MODERATE","136/449",2,{"$nulls":5},"5","866","446","643","327","781","407","0","0","0","0.1671",{"$nulls":20},"0.683534","2.93",null,"1","-0.95;-0.97;-0.97","0.004;.;0.988","0.193;0.233;0.168","0.044;0.038;0.042",{"$nulls":3},"1000Gp3_AFR_AF",0.01664145234493192,{"$nulls":7},"0/0","853,0","0","853","0/1","357,71","0.1659","428",null,"chr12:113207761:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1743"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ITGAL","chr16:30494775","ITGAL(E476D)",null,null,"topological domain (Extracellular ), repeat (FG-GAP 5 ), calcium-binding region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrin alpha-L/beta-2 is also a receptor for F11R (PubMed:11812992, PubMed:15528364). Involved in a variety of immune phenomena including leukocyte-endothelial cell interaction, cytotoxic T-cell mediated killing, and antibody dependent killing by granulocytes and monocytes. Contributes to natural killer cell cytotoxicity (PubMed:15356110). Involved in leukocyte adhesion and transmigration of leukocytes including T-cells and neutrophils (PubMed:11812992). Required for generation of common lymphoid progenitor cells in bone marrow, indicating a role in lymphopoiesis (By similarity). Integrin alpha-L/beta-2 in association with ICAM3, contributes to apoptotic neutrophil phagocytosis by macrophages (PubMed:23775590). {ECO:0000250|UniProtKB:P24063, ECO:0000269|PubMed:11812992, ECO:0000269|PubMed:15356110, ECO:0000269|PubMed:15528364, ECO:0000269|PubMed:23775590}.; ",{"$nulls":4},"p.Glu476Asp","c.1428G>T","MODERATE","476/1170",13,{"$nulls":5},"5","771","455","512","302","724","418","0","0","0","0.1411",{"$nulls":20},"0.947679","1.29","-0.605;.","1;0.787649;0.878567","1.14","0.008;.","1.0","0.302;0.299",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","733,0","0","733","0/1","353,68","0.1615","421",null,"chr16:30494775:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1623"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ITGB5","chr3:124773816","ITGB5(R597T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Integrin alpha-V/beta-5 (ITGAV:ITGB5) is a receptor for fibronectin. It recognizes the sequence R-G-D in its ligand.; ",{"$nulls":4},"p.Arg597Thr","c.1790G>C","MODERATE","597/799",11,{"$nulls":5},"5","1299","571","945","397","1130","488","0","0","0","0.1885",{"$nulls":20},"1.620861","-3.05","-0.25","0.999999","0.42","0.008","0.281","0.239",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1249,0","0","1249","0/1","426,99","0.1886","525",null,"chr3:124773816:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1839"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ITPKC","chr19:40717958","ITPKC(G275R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Can phosphorylate inositol 2,4,5-triphosphate to inositol 2,4,5,6-tetraphosphate. {ECO:0000250}.; ",{"$nulls":4},"p.Gly275Arg","c.823G>C","MODERATE","275/683",1,{"$nulls":5},"4","748","388","636","319","502","270","0","0","0","0.1889",{"$nulls":20},"2.179038",null,"1.79","1","-1.16","0.845","0.001","0.289",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)] 3-kinase family of enzymes that catalyze the phosphorylation of inositol 1,4,5-trisphosphate to 1,3,4,5-tetrakisphosphate. The encoded protein is localized to the nucleus and cytoplasm and has both nuclear import and nuclear export activity. Single nucleotide polymorphisms in this gene are associated with Kawasaki disease.[provided by RefSeq, Sep 2009].  ",null,null,"0/0","747,0","0","747","0/1","315,66","0.1732","381",null,"chr19:40717958:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1724"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KCNJ3","chr2:154855003","KCNJ3(L399Q)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: This potassium channel is controlled by G proteins. Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. Their voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium. This receptor plays a crucial role in regulating the heartbeat.; ",{"$nulls":4},"p.Leu399Gln","c.1196T>A","MODERATE","399/501",3,{"$nulls":5},"4","538","346",null,null,"495","306","0","0","0","0.1176",{"$nulls":20},"3.3999639999999998","-3.18","2.3","0.999954;1","0.04","0.624","0.001","0.358",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0|0","547,0","0","547","0|1","304,45","0.1289","349",null,"chr2:154855003:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KCNJ3","chr2:154855006","KCNJ3(P400Q)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: This potassium channel is controlled by G proteins. Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. Their voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium. This receptor plays a crucial role in regulating the heartbeat.; ",{"$nulls":4},"p.Pro400Gln","c.1199C>A","MODERATE","400/501",3,{"$nulls":5},"4","533","344",null,null,"490","310","0.0019","0.0019","0","0.1194",{"$nulls":20},"3.690772","-3.48","2.3","1","-1.5","1.0",null,"0.616",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0|0","542,0","0","542","0|1","300,45","0.1304","345",null,"chr2:154855006:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KLHDC7A","chr1:18482954","KLHDC7A(W658*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Trp658*","c.1973G>A","HIGH","658/777",1,{"$nulls":5},"5","1133","569","971","485","977","497","0","0","0","0.161",{"$nulls":20},"7.834579",null,null,"1",{"$nulls":3},"0.038",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1101,0","0","1101","0/1","457,88","0.1615","545",null,"chr1:18482954:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.167"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KLHL12","chr1:202896947","KLHL12(V282V)",{"$nulls":3},"repeat:Kelch_1","LOW",null,255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a negative regulator of Wnt signaling pathway and ER-Golgi transport (PubMed:22358839, PubMed:27565346). The BCR(KLHL12) complex is involved in ER-Golgi transport by regulating the size of COPII coats, thereby playing a key role in collagen export, which is required for embryonic stem (ES) cells division: BCR(KLHL12) acts by mediating monoubiquitination of SEC31 (SEC31A or SEC31B) (PubMed:22358839, PubMed:27565346). The BCR(KLHL12) complex is also involved in neural crest specification: in response to cytosolic calcium increase, interacts with the heterodimer formed with PEF1 and PDCD6/ALG-2, leading to bridge together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export (PubMed:27716508). As part of the BCR(KLHL12) complex, also acts as a negative regulator of the Wnt signaling pathway by mediating ubiquitination and subsequent proteolysis of DVL3 (PubMed:16547521). The BCR(KLHL12) complex also mediates polyubiquitination of DRD4 and PEF1, without leading to degradation of these proteins (PubMed:18303015, PubMed:20100572, PubMed:27716508). {ECO:0000269|PubMed:16547521, ECO:0000269|PubMed:18303015, ECO:0000269|PubMed:20100572, ECO:0000269|PubMed:22358839, ECO:0000269|PubMed:27565346, ECO:0000269|PubMed:27716508}.; ",{"$nulls":5},"c.846G>T","HIGH",null,7,{"$nulls":5},"3","690","474","470","303",null,null,"0.0014","0.0014",{"$nulls":33},"Unknown",-1,{"$nulls":7},"0/0","681,1","0.0015","682","0/1","387,56","0.1264","443",null,"chr1:202896947:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1221"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KLRC4","chr12:10407703","KLRC4(E143*)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May play a role as a receptor for the recognition of MHC class I HLA-E molecules by NK cells.; ",{"$nulls":4},"p.Glu143*","c.427G>T","HIGH","143/158",4,{"$nulls":5},"5","442","631","329","468","351","502","0","0","0","0.0916",{"$nulls":20},"6.418128",null,null,"0.984521",{"$nulls":3},"0.048",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","432,0","0","432","0/1","558,52","0.0852","610",null,"chr12:10407703:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.094"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","KMT2C","chr7:152202991","KMT2C(K1346fs)",null,null,"coiled-coil region , sequence variant (In KLEFS2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Kleefstra syndrome 2 (KLEFS2) [MIM:617768]: A form of Kleefstra syndrome, an autosomal dominant disease characterized by variable mental retardation, psychomotor developmental delay, seizures, behavioral abnormalities, and facial dysmorphisms. {ECO:0000269|PubMed:22726846, ECO:0000269|PubMed:29069077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Histone methyltransferase. Methylates 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Central component of the MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. KMT2C/MLL3 may be a catalytic subunit of this complex. May be involved in leukemogenesis and developmental disorder. {ECO:0000269|PubMed:17500065}.; ",{"$nulls":4},"p.Lys1346fs","c.4034dupA","HIGH","1345/4911",26,{"$nulls":5},"5","137","114","95","74","109","86","0","0","0","0.093",{"$nulls":5},"(KMT2C|ENSG00000055609|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008].  ",null,"C4540395","0/0","129,0","0","129","0/1","87,14","0.1386","101",null,"chr7:152202991:C:CT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1351"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KMT2C","chr7:152202991","KMT2C(K1346fs)",null,null,"coiled-coil region , sequence variant (In KLEFS2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Kleefstra syndrome 2 (KLEFS2) [MIM:617768]: A form of Kleefstra syndrome, an autosomal dominant disease characterized by variable mental retardation, psychomotor developmental delay, seizures, behavioral abnormalities, and facial dysmorphisms. {ECO:0000269|PubMed:22726846, ECO:0000269|PubMed:29069077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Histone methyltransferase. Methylates 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Central component of the MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. KMT2C/MLL3 may be a catalytic subunit of this complex. May be involved in leukemogenesis and developmental disorder. {ECO:0000269|PubMed:17500065}.; ",{"$nulls":4},"p.Lys1346fs","c.4034dupA","HIGH","1345/4911",26,{"$nulls":5},"5","137","97","95","58","109","84","0","0","0","0.4762",{"$nulls":5},"(KMT2C|ENSG00000055609|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008].  ",null,"C4540395","0/0","128,0","0","128","0/1","38,53","0.5824","91",null,"chr7:152202991:C:CT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","KMT2C","chr7:152176752","KMT2C(P2901A)",null,null,"sequence variant (In KLEFS2. ), sequence variant (In KLEFS2. ), sequence variant (In KLEFS2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Kleefstra syndrome 2 (KLEFS2) [MIM:617768]: A form of Kleefstra syndrome, an autosomal dominant disease characterized by variable mental retardation, psychomotor developmental delay, seizures, behavioral abnormalities, and facial dysmorphisms. {ECO:0000269|PubMed:22726846, ECO:0000269|PubMed:29069077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Histone methyltransferase. Methylates 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Central component of the MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. KMT2C/MLL3 may be a catalytic subunit of this complex. May be involved in leukemogenesis and developmental disorder. {ECO:0000269|PubMed:17500065}.; ",{"$nulls":4},"p.Pro2901Ala","c.8701C>G","MODERATE","2901/4911",38,{"$nulls":5},"5","1021","679","816","542","874","567","0","0","0","0.1393",{"$nulls":20},"1.480969","-2.94;-2.98","2.19","0.987944","-5.03;-5.29","0.0","0.057;0.055","0.1;0.126",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008].  ",null,"C4540395","0/0","1014,0","0","1014","0/1","576,93","0.139","669",null,"chr7:152176752:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1273"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","LGALS9B","chr17:20467461","LGALS9B(S4R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds galactosides. {ECO:0000250}.; ",{"$nulls":4},"p.Ser4Arg","c.10A>C","MODERATE","4/356",1,{"$nulls":5},"3","58","24","91","31",null,null,"0","0",{"$nulls":22},"0.386629","3.95","1.145","1","-2.03","0.004;0.003","0.345","0.15;0.151",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","58,0","0","58","0/1","18,6","0.25","24",null,"chr17:20467461:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.2258"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","LGALS9C","chr17:18476864","LGALS9C(S4R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds galactosides. {ECO:0000250}.; ",{"$nulls":4},"p.Ser4Arg","c.10A>C","MODERATE","4/356",1,{"$nulls":5},"3",null,null,"792","378","751","374",null,null,"0","0.0775",{"$nulls":20},"0.2867","3.69;3.75;3.93;3.83;3.92",".;.;1.21;.;.","1;1;1;1;0.993855",".;.;-2.13;.;.",".;.;0.007;.;.",".;.;0.345;.;.","0.151;.;0.139;0.17;0.172",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1009,0","0","1009","0/1","461,43","0.0853","504",null,"chr17:18476864:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0794"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","LGI1","chr10:93797409","LGI1(P427L)",null,null,"repeat (EAR 5 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Epilepsy, familial temporal lobe, 1 (ETL1) [MIM:600512]: A focal form of epilepsy characterized by recurrent seizures that arise from foci within the temporal lobe. Seizures are usually accompanied by sensory symptoms, most often auditory in nature. {ECO:0000269|PubMed:11810107, ECO:0000269|PubMed:12205652, ECO:0000269|PubMed:12601709, ECO:0000269|PubMed:12771268, ECO:0000269|PubMed:15079010, ECO:0000269|PubMed:17067999, ECO:0000269|PubMed:17296837, ECO:0000269|PubMed:17562837, ECO:0000269|PubMed:18625862, ECO:0000269|PubMed:19552651}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Regulates voltage-gated potassium channels assembled from KCNA1, KCNA4 and KCNAB1. It slows down channel inactivation by precluding channel closure mediated by the KCNAB1 subunit. Ligand for ADAM22 that positively regulates synaptic transmission mediated by AMPA-type glutamate receptors (By similarity). Plays a role in suppressing the production of MMP1/3 through the phosphatidylinositol 3-kinase/ERK pathway. May play a role in the control of neuroblastoma cell survival. {ECO:0000250, ECO:0000269|PubMed:15047712, ECO:0000269|PubMed:16518856}.; ","epilepsy",{"$nulls":3},"p.Pro427Leu","c.1280C>T","MODERATE","427/557",8,{"$nulls":5},"5","1196","533","958","397","999","446","0","0","0","0.1906",{"$nulls":20},"3.609555","-1.83;.;.","2.415;.;.","1","-6.29;.;.","0.875;.;0.973","0.002;.;.","0.414;0.477;0.522",{"$nulls":3},"Unknown",-1,"AD","Epilepsy, familial temporal lobe, 1","Neurologic",{"$nulls":3},"C4551957","0/0","1189,0","0","1189","0/1","430,101","0.1902","531",null,"chr10:93797409:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1889"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","LMTK3","chr19:48497476","LMTK3(P1227H)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Protein kinase which phosphorylates ESR1 (in vitro) and protects it against proteasomal degradation. May also regulate ESR1 levels indirectly via a PKC-AKT-FOXO3 pathway where it decreases the activity of PKC and the phosphorylation of AKT, thereby increasing binding of transcriptional activator FOXO3 to the ESR1 promoter and increasing ESR1 transcription (PubMed:21602804). Involved in endocytic trafficking of N-methyl- D-aspartate receptors (NMDAR) in neurons (By similarity). {ECO:0000250|UniProtKB:Q5XJV6, ECO:0000269|PubMed:21602804}.; ",null,"[ \"Tamoxifen\" , \"Toremifene\"]","[ \"Tamoxifen\" , \"Toremifene\"]","[ \"Tamoxifen\" , \"Toremifene\"]","p.Pro1227His","c.3680C>A","MODERATE","1227/1489",12,{"$nulls":5},"5","528","184","372","133","464","166","0","0","0","0.2289",{"$nulls":20},"2.558637","-1.16;-1.16;.","0.695;.;.","0.999747",".;-2.52;.","0.698;.;.",".;0.013;.","0.169;0.143;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","515,0","0","515","0/1","134,40","0.2299","174",null,"chr19:48497476:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2406"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","LRRC49","chr15:71008563","LRRC49(D457H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp457His","c.1369G>C","MODERATE","457/691",12,{"$nulls":5},"4","465","308","308","227","432","281","0","0","0","0.0641",{"$nulls":20},"3.869938","0.94;0.93;0.94;0.94;.;.",".;.;.;2.295;.;.","0.999987;0.999987;0.999987;0.999997;0.999997;0.999987","-3.46;-3.46;-3.23;-3.46;-3.06;-3.06",".;.;.;0.997;.;.","0.007;0.007;0.006;0.007;0.002;0.002","0.887;0.872;0.921;0.904;0.859;0.857",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","462,0","0","462","0/1","282,21","0.0693","303",null,"chr15:71008563:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0793"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","LRRC49","chr15:71008563","LRRC49(D457H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp457His","c.1369G>C","MODERATE","457/691",12,{"$nulls":5},"4","465","324","308","227","434","302","0","0","0","0.3113",{"$nulls":20},"3.869938","0.94;0.93;0.94;0.94;.;.",".;.;.;2.295;.;.","0.999987;0.999987;0.999987;0.999997;0.999997;0.999987","-3.46;-3.46;-3.23;-3.46;-3.06;-3.06",".;.;.;0.997;.;.","0.007;0.007;0.006;0.007;0.002;0.002","0.887;0.872;0.921;0.904;0.859;0.857",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","461,0","0","461","0/1","220,99","0.3103","319",null,"chr15:71008563:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3172"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","LTBP2","chr14:74528991","LTBP2(S707fs)",null,null,"domain (TB 2 ), disulfide bond , disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Glaucoma 3, primary congenital, D (GLC3D) [MIM:613086]: An autosomal recessive form of primary congenital glaucoma (PCG). PCG is characterized by marked increase of intraocular pressure at birth or early childhood, large ocular globes (buphthalmos) and corneal edema. It results from developmental defects of the trabecular meshwork and anterior chamber angle of the eye that prevent adequate drainage of aqueous humor. {ECO:0000269|PubMed:19361779}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma (MSPKA) [MIM:251750]: A rare disease characterized by smaller and more spherical lenses than normal bilaterally, an increased anteroposterior thickness of the lens, and highly myopic eyes. Lens dislocation or subluxation may occur, leading to defective accommodation. {ECO:0000269|PubMed:20617341}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Weill-Marchesani syndrome 3 (WMS3) [MIM:614819]: A rare connective tissue disorder characterized by short stature, brachydactyly, joint stiffness, and eye abnormalities including microspherophakia, ectopia lentis, severe myopia and glaucoma. {ECO:0000269|PubMed:22539340}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May play an integral structural role in elastic-fiber architectural organization and/or assembly. {ECO:0000303|PubMed:10743502, ECO:0000303|PubMed:11104663}.; ",{"$nulls":4},"p.Ser707fs","c.2118delC","HIGH","706/1821",11,{"$nulls":5},"4","1087","420","881","329","952","356","0","0","0","0.1713",{"$nulls":5},"(LTBP2|ENSG00000119681|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Glaucoma 3, primary congenital, D; Microspherophakia and/or megalocornea, with ectopia lentis and with or without secondary glaucoma; Weill-Marchesani syndrome 3","Cardiovascular; Craniofacial; Musculoskeletal; Ophthalmologic",{"$nulls":3},"C3538951| C2751316| C3553785| C1832977","0/0","1046,0","0","1046","0/1","327,71","0.1784","398",null,"chr14:74528991:TG:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1702"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MASP1","chr3:187285843","MASP1(C73W)",null,null,"domain (CUB 1 ), region of interest (Interaction with FCN2 ), region of interest (Homodimerization ), region of interest (Interaction with MBL2 ), disulfide bond , splice variant (In isoform 4. ), sequence variant (In 3MC1. ), helix ","disulfide-bond:experimental_evidence_used_in_manual_assertion","MODERATE",null,255,"PASS","Missense",null,-1,"DISEASE: 3MC syndrome 1 (3MC1) [MIM:257920]: A form of 3MC syndrome, an autosomal recessive disorder characterized by facial dysmorphism, craniosynostosis, learning disability, and genital, limb and vesicorenal anomalies. Facial features include hypertelorism, blepharophimosis, blepharoptosis and highly arched eyebrows, cleft lip and/or palate. The term 3MC syndrome includes Carnevale, Mingarelli, Malpuech, and Michels syndromes. {ECO:0000269|PubMed:21258343, ECO:0000269|PubMed:26419238, ECO:0000269|PubMed:28301481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Functions in the lectin pathway of complement, which performs a key role in innate immunity by recognizing pathogens through patterns of sugar moieties and neutralizing them. The lectin pathway is triggered upon binding of mannan-binding lectin (MBL) and ficolins to sugar moieties which leads to activation of the associated proteases MASP1 and MASP2. Functions as an endopeptidase and may activate MASP2 or C2 or directly activate C3 the key component of complement reaction. Isoform 2 may have an inhibitory effect on the activation of the lectin pathway of complement or may cleave IGFBP5. Also plays a role in development (PubMed:21258343). {ECO:0000269|PubMed:11485744, ECO:0000269|PubMed:21258343}.; ",{"$nulls":4},"p.Cys73Trp","c.219T>G","MODERATE","73/728",2,{"$nulls":5},"5","395","325","350","274","306","252","0","0","0","0.1151",{"$nulls":20},"3.920211","1.48","4.82;4.82;4.82;.;.;.;.","1","-10.28;-10.34;-10.8;-10.8;-10.88;-11.0;-11.0","1.0;1.0;1.0;1.0;.;.;.","0.0","0.926;0.931;0.925;0.911;.;.;.",{"$nulls":3},"Unknown",-1,"AR","3MC syndrome 1","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic ",{"$nulls":3},"C0796059","0|0","413,0","0","413","0|1","291,37","0.1128","328",null,"chr3:187285843:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1022"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MASP1","chr3:187285847","MASP1(L72fs)",null,null,"domain (CUB 1 ), region of interest (Interaction with FCN2 ), region of interest (Homodimerization ), region of interest (Interaction with MBL2 ), splice variant (In isoform 4. ), sequence variant (In 3MC1. ), helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: 3MC syndrome 1 (3MC1) [MIM:257920]: A form of 3MC syndrome, an autosomal recessive disorder characterized by facial dysmorphism, craniosynostosis, learning disability, and genital, limb and vesicorenal anomalies. Facial features include hypertelorism, blepharophimosis, blepharoptosis and highly arched eyebrows, cleft lip and/or palate. The term 3MC syndrome includes Carnevale, Mingarelli, Malpuech, and Michels syndromes. {ECO:0000269|PubMed:21258343, ECO:0000269|PubMed:26419238, ECO:0000269|PubMed:28301481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Functions in the lectin pathway of complement, which performs a key role in innate immunity by recognizing pathogens through patterns of sugar moieties and neutralizing them. The lectin pathway is triggered upon binding of mannan-binding lectin (MBL) and ficolins to sugar moieties which leads to activation of the associated proteases MASP1 and MASP2. Functions as an endopeptidase and may activate MASP2 or C2 or directly activate C3 the key component of complement reaction. Isoform 2 may have an inhibitory effect on the activation of the lectin pathway of complement or may cleave IGFBP5. Also plays a role in development (PubMed:21258343). {ECO:0000269|PubMed:11485744, ECO:0000269|PubMed:21258343}.; ",{"$nulls":4},"p.Leu72fs","c.214delC","HIGH","72/728",2,{"$nulls":5},"5","423","349","370","293","356","295","0","0","0","0.0983",{"$nulls":5},"(MASP1|ENSG00000127241|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","3MC syndrome 1","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic ",{"$nulls":3},"C0796059","0|0","435,0","0","435","0|1","310,37","0.1066","347",null,"chr3:187285847:AG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0887"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MBOAT4","chr8:30132252","MBOAT4(F333L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the octanoylation of ghrelin at 'Ser-3'. Can use a variety of fatty acids as substrates including octanoic acid, decanoic acid and tetradecanoic acid. {ECO:0000269|PubMed:18443287}.; ",{"$nulls":4},"p.Phe333Leu","c.999C>A","MODERATE","333/435",3,{"$nulls":5},"4","809","635","669","511","668","528","0","0","0","0.1061",{"$nulls":20},"3.220634","-0.58","2.36","1;1;0.991183","1.0","0.081","0.477","0.333",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","806,0","0","806","0/1","557,67","0.1074","624",null,"chr8:30132252:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1076"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","MCF2L2","chr3:183289165","MCF2L2(L577F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably functions as a guanine nucleotide exchange factor. {ECO:0000250}.; ",{"$nulls":4},"p.Leu577Phe","c.1731G>C","MODERATE","577/1114",14,{"$nulls":5},"5","627","402","433","260","558","366","0","0","0","0.0765",{"$nulls":20},"0.588961","4.54;4.56;3.66;3.41","1.95","1","-1.57;-1.57;-1.57;-1.93","0.917;.;0.008;.","0.304;0.352;0.494;0.049","0.045;0.048;0.05;0.068",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","608,0","0","608","0/1","345,31","0.0824","376",null,"chr3:183289165:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0808"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MCF2L2","chr3:183289165","MCF2L2(L577F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probably functions as a guanine nucleotide exchange factor. {ECO:0000250}.; ",{"$nulls":4},"p.Leu577Phe","c.1731G>C","MODERATE","577/1114",14,{"$nulls":5},"5","627","511","433","337","556","454","0","0","0","0.1586",{"$nulls":20},"0.588961","4.54;4.56;3.66;3.41","1.95","1","-1.57;-1.57;-1.57;-1.93","0.917;.;0.008;.","0.304;0.352;0.494;0.049","0.045;0.048;0.05;0.068",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","603,0","0","603","0/1","389,83","0.1758","472",null,"chr3:183289165:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1721"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MDH1B","chr2:206750990","MDH1B(S332fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ser332fs","c.994_995delAG","HIGH","332/518",6,{"$nulls":5},"4","584","337","400","233","504","298","0","0","0","0.1477",{"$nulls":5},"(MDH1B|ENSG00000138400|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","558,0","0","558","0/1","256,49","0.1607","305",null,"chr2:206750990:ACT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1416"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MEP1B","chr18:32208231","MEP1B(E296fs)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Membrane metallopeptidase that sheds many membrane-bound proteins. Exhibits a strong preference for acidic amino acids at the P1' position. Known substrates include: FGF19, VGFA, IL1B, IL18, procollagen I and III, E-cadherin, KLK7, gastrin, ADAM10, tenascin-C. The presence of several pro-inflammatory cytokine among substrates implicate MEP1B in inflammation. It is also involved in tissue remodeling due to its capability to degrade extracellular matrix components. {ECO:0000269|PubMed:21693781}.; ",{"$nulls":4},"p.Glu296fs","c.887_912delAGAGTGATCACTCCAACATGGGCCAG","HIGH","296/701",9,{"$nulls":5},"4","619","363","405","248","409","243","0","0","0","0.214",{"$nulls":5},"(MEP1B|ENSG00000141434|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","596,0","0","596","0/1","284,51","0.1522","335",null,"chr18:32208231:GGGGCCAGAGAGTGATCACTCCAACAT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1613"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","METTL4","chr18:2566967","METTL4(R84G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable methyltransferase. {ECO:0000250}.; ",{"$nulls":4},"p.Arg84Gly","c.250C>G","MODERATE","84/472",2,{"$nulls":5},"5","585","320","421","232","538","284","0","0","0","0.1373",{"$nulls":20},"2.04763","1.91;2.25",".;0","1","-0.98;.",".;0.001","0.026;.","0.171;0.12",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","583,0","0","583","0/1","269,48","0.1514","317",null,"chr18:2566967:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1595"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MLLT3","chr9:20414111","MLLT3(E245D)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving MLLT3 is associated with acute leukemias. Translocation t(9;11)(p22;q23) with KMT2A/MLL1. The result is a rogue activator protein. {ECO:0000269|PubMed:10861294, ECO:0000269|PubMed:8506309}.; DISEASE: Note=A chromosomal aberration involving MLLT3 was observed in a patient with neuromotor development delay, cerebellar ataxia and epilepsy. Translocation t(4;9)(q35;p22). {ECO:0000269|PubMed:16001262}.; ","FUNCTION: Chromatin reader component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA (PubMed:20159561, PubMed:20471948, PubMed:25417107, PubMed:27105114, PubMed:27545619). Specifically recognizes and binds acylated histone H3, with a marked preference for histone H3 that is crotonylated (PubMed:25417107, PubMed:27105114, PubMed:27545619). Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors (PubMed:25417107, PubMed:27105114, PubMed:27545619). Recognizes and binds histone H3 crotonylated at 'Lys-9' (H3K9cr), and with slightly lower affinity histone H3 crotonylated at 'Lys-18' (H3K18cr) (PubMed:27105114). Also recognizes and binds histone H3 acetylated at 'Lys-9' (H3K9ac), but with lower affinity than crotonylated histone H3 (PubMed:25417107, PubMed:27105114). In the SEC complex, MLLT3 is required to recruit the complex to crotonylated histones (PubMed:27105114, PubMed:27545619). {ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:25417107, ECO:0000269|PubMed:27105114, ECO:0000269|PubMed:27545619}.; ","level2",{"$nulls":3},"p.Glu245Asp","c.735G>C","MODERATE","245/568",5,1,{"$nulls":4},"4","1660","784","1315","606","1347","606","0","0","0","0.1667",{"$nulls":20},"1.369407",null,"1.23;.","0.966459;0.966459;1","-0.88;.","0.009;.","0.167;.","0.149;0.143",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","1653,0","0","1653","0/1","634,133","0.1734","767",null,"chr9:20414111:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1716"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MUC3A","chr7:100952051","MUC3A(L91*)",null,null,"compositionally biased region (Thr-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Major glycoprotein component of a variety of mucus gels. Thought to provide a protective, lubricating barrier against particles and infectious agents at mucosal surfaces. May be involved in ligand binding and intracellular signaling. {ECO:0000269|PubMed:10405327}.; ",{"$nulls":4},"p.Leu91*","c.272T>A","HIGH","91/3323",2,{"$nulls":5},"4","1978","1085","1587","843","1681","893","0","0","0","0.0862",{"$nulls":5},"(MUC3A|ENSG00000169894|1|1.00)","(MUC3A|ENSG00000169894|1|1.00)",{"$nulls":13},"3.970598",{"$nulls":6},"0.098;0.107",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1960,0","0","1960","0/1","952,89","0.0855","1041",null,"chr7:100952051:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0866"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","MYF5","chr12:80717124","MYF5(I21V)",{"$nulls":6},255,"PASS","Missense","rs371882555",0.0002915,null,"FUNCTION: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with MYOG and MYOD1, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Probable sequence specific DNA-binding protein.; ",{"$nulls":4},"p.Ile21Val","c.61A>G","MODERATE","21/255",1,1,{"$nulls":4},"4","854","464","637","340",null,null,"0","0",{"$nulls":22},"2.225698","-1.01","1.87","0.636769","-0.56","0.124","0.109","0.276",{"$nulls":3},"ExAC_AFR_AF",0.0002915,{"$nulls":6},"C4748418","0/0","828,0","0","828","0/1","410,26","0.0596","436",null,"chr12:80717124:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MYF5","chr12:80717124","MYF5(I21V)",{"$nulls":6},255,"PASS","Missense","rs371882555",0.0002915,null,"FUNCTION: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with MYOG and MYOD1, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Probable sequence specific DNA-binding protein.; ",{"$nulls":4},"p.Ile21Val","c.61A>G","MODERATE","21/255",1,1,{"$nulls":4},"5","854","395","637","287","755","348","0","0","0","0.2241",{"$nulls":20},"2.225698","-1.01","1.87","0.636769","-0.56","0.124","0.109","0.276",{"$nulls":3},"ExAC_AFR_AF",0.0002915,{"$nulls":6},"C4748418","0/0","828,0","0","828","0/1","292,77","0.2087","369",null,"chr12:80717124:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2056"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MYO3B","chr2:170400313","MYO3B(N639K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable actin-based motor with a protein kinase activity. Required for normal cochlear hair bundle development and hearing. Plays an important role in the early steps of cochlear hair bundle morphogenesis. Influences the number and lengths of stereocilia to be produced and limits the growth of microvilli within the forming auditory hair bundles thereby contributing to the architecture of the hair bundle, including its staircase pattern. Involved in the elongation of actin in stereocilia tips by transporting the actin regulatory factor ESPN to the plus ends of actin filaments. {ECO:0000250|UniProtKB:Q1EG27}.; ",{"$nulls":4},"p.Asn639Lys","c.1917T>G","MODERATE","639/1341",17,{"$nulls":5},"4","421","282","297","188","370","247","0","0","0","0.247",{"$nulls":20},"2.037634","-2.11","-0.125;-0.125;.","0.999951","-2.56","0.041;0.592;.","0.411;0.485;0.599","0.814;0.808;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","420,0","0","420","0/1","199,80","0.2867","279",null,"chr2:170400313:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2979"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","MYOM1","chr18:3100404","MYOM1(L1200F)",{"$nulls":6},255,"PASS","Missense","rs1039058791",-1,null,"FUNCTION: Major component of the vertebrate myofibrillar M band. Binds myosin, titin, and light meromyosin. This binding is dose dependent.; ",{"$nulls":4},"p.Leu1200Phe","c.3598C>T","MODERATE","1200/1685",24,{"$nulls":5},"5","515","303","354","194","490","283","0","0","0","0.1802",{"$nulls":20},"3.067136","-0.33;.;-0.33","1.935;.;.","0.999998;0.999949;0.999998","-1.56;.;-1.59","0.998;.;0.995","0.185;.;0.032","0.501;0.556;0.538",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The giant protein titin, together with its associated proteins, interconnects the major structure of sarcomeres, the M bands and Z discs. The C-terminal end of the titin string extends into the M line, where it binds tightly to M-band constituents of apparent molecular masses of 190 kD (myomesin 1) and 165 kD (myomesin 2). This protein, myomesin 1, like myomesin 2, titin, and other myofibrillar proteins contains structural modules with strong homology to either fibronectin type III (motif I) or immunoglobulin C2 (motif II) domains. Myomesin 1 and myomesin 2 each have a unique N-terminal region followed by 12 modules of motif I or motif II, in the arrangement II-II-I-I-I-I-I-II-II-II-II-II. The two proteins share 50% sequence identity in this repeat-containing region. The head structure formed by these 2 proteins on one end of the titin string extends into the center of the M band. The integrating structure of the sarcomere arises from muscle-specific members of the superfamily of immunoglobulin-like proteins. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008].",null,null,"0/0","494,0","0","494","0/1","228,51","0.1828","279",null,"chr18:3100404:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1753"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","NAALADL2","chr3:175576066","NAALADL2(R560I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be catalytically inactive.; ",{"$nulls":4},"p.Arg560Ile","c.1679_1680delGAinsTT","MODERATE","560/795",10,{"$nulls":5},"4","428","266","366","215","354","223","0","0","0","0.0807",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","425,0","0","425","0/1","234,20","0.0787","254",null,"chr3:175576066:GA:TT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0791"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","NAALADL2","chr3:175576066","NAALADL2(R560I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be catalytically inactive.; ",{"$nulls":4},"p.Arg560Ile","c.1679_1680delGAinsTT","MODERATE","560/795",10,{"$nulls":5},"5","428","357","366","296","363","320","0","0","0","0.1938",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","425,0","0","425","0/1","288,69","0.1933","357",null,"chr3:175576066:GA:TT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1993"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","NOS1","chr12:117255982","NOS1(D863Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Produces nitric oxide (NO) which is a messenger molecule with diverse functions throughout the body. In the brain and peripheral nervous system, NO displays many properties of a neurotransmitter. Probably has nitrosylase activity and mediates cysteine S-nitrosylation of cytoplasmic target proteins such SRR.; ",{"$nulls":4},"p.Asp863Tyr","c.2587G>T","MODERATE","863/1468",16,{"$nulls":5},"5","1062","606","780","419","959","537","0.0009","0.0009","0","0.1061",{"$nulls":20},"1.7909920000000001",".;4.95",null,"1",".;-0.55",null,".;0.097","0.337;0.315",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1012,0","0","1012","0/1","500,64","0.1135","564",null,"chr12:117255982:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1146"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","NOX1","chrX:100848637","NOX1(H521D)",null,null,"topological domain (Cytoplasmic ), region of interest (Interaction with NOXO1 ), splice variant (In isoform NOH-1S. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: NOH-1S is a voltage-gated proton channel that mediates the H(+) currents of resting phagocytes and other tissues. It participates in the regulation of cellular pH and is blocked by zinc. NOH-1L is a pyridine nucleotide-dependent oxidoreductase that generates superoxide and might conduct H(+) ions as part of its electron transport mechanism, whereas NOH-1S does not contain an electron transport chain.; ",{"$nulls":4},"p.His521Asp","c.1561C>G","MODERATE","521/564",12,{"$nulls":5},"5","744","389","576","292","596","312","0","0","0","0.1538",{"$nulls":20},"3.094054","-3.63","2.37;.;.","0.931727;0.931727;0.931727;0.999999","-7.22;-7.19;-7.21","0.836;0.782;0.661","0.006;0.005;0.005","0.622;0.613;0.609",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","726,0","0","726","0/1","311,54","0.1479","365",null,"chrX:100848637:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.137"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","NTRK1","chr1:156860942","NTRK1(R3P)",null,null,"signal peptide , splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Congenital insensitivity to pain with anhidrosis (CIPA) [MIM:256800]: Characterized by a congenital insensitivity to pain, anhidrosis (absence of sweating), absence of reaction to noxious stimuli, self-mutilating behavior, and mental retardation. This rare autosomal recessive disorder is also known as congenital sensory neuropathy with anhidrosis or hereditary sensory and autonomic neuropathy type IV or familial dysautonomia type II. {ECO:0000269|PubMed:10090906, ECO:0000269|PubMed:10233776, ECO:0000269|PubMed:10330344, ECO:0000269|PubMed:10567924, ECO:0000269|PubMed:10861667, ECO:0000269|PubMed:10982191, ECO:0000269|PubMed:11159935, ECO:0000269|PubMed:11310631, ECO:0000269|PubMed:18077166, ECO:0000269|PubMed:22302274, ECO:0000269|PubMed:27676246, ECO:0000269|PubMed:28177573, ECO:0000269|PubMed:28328124, ECO:0000269|PubMed:8696348}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Chromosomal aberrations involving NTRK1 are found in papillary thyroid carcinomas (PTCs) (PubMed:2869410, PubMed:7565764, PubMed:1532241). Translocation t(1;3)(q21;q11) with TFG generates the TRKT3 (TRK-T3) transcript by fusing TFG to the 3'-end of NTRK1 (PubMed:7565764). A rearrangement with TPM3 generates the TRK transcript by fusing TPM3 to the 3'-end of NTRK1 (PubMed:2869410). An intrachromosomal rearrangement that links the protein kinase domain of NTRK1 to the 5'-end of the TPR gene forms the fusion protein TRK-T1. TRK-T1 is a 55 kDa protein reacting with antibodies against the C-terminus of the NTRK1 protein (PubMed:1532241). {ECO:0000269|PubMed:1532241, ECO:0000269|PubMed:2869410, ECO:0000269|PubMed:7565764}.; ","FUNCTION: Receptor tyrosine kinase involved in the development and the maturation of the central and peripheral nervous systems through regulation of proliferation, differentiation and survival of sympathetic and nervous neurons. High affinity receptor for NGF which is its primary ligand (PubMed:1850821, PubMed:1849459, PubMed:1281417, PubMed:8325889, PubMed:15488758, PubMed:17196528, PubMed:27445338). Can also bind and be activated by NTF3/neurotrophin-3. However, NTF3 only supports axonal extension through NTRK1 but has no effect on neuron survival (By similarity). Upon dimeric NGF ligand-binding, undergoes homodimerization, autophosphorylation and activation (PubMed:1281417). Recruits, phosphorylates and/or activates several downstream effectors including SHC1, FRS2, SH2B1, SH2B2 and PLCG1 that regulate distinct overlapping signaling cascades driving cell survival and differentiation. Through SHC1 and FRS2 activates a GRB2-Ras-MAPK cascade that regulates cell differentiation and survival. Through PLCG1 controls NF-Kappa-B activation and the transcription of genes involved in cell survival. Through SHC1 and SH2B1 controls a Ras-PI3 kinase-AKT1 signaling cascade that is also regulating survival. In absence of ligand and activation, may promote cell death, making the survival of neurons dependent on trophic factors. {ECO:0000250|UniProtKB:P35739, ECO:0000250|UniProtKB:Q3UFB7, ECO:0000269|PubMed:11244088, ECO:0000269|PubMed:1281417, ECO:0000269|PubMed:15488758, ECO:0000269|PubMed:17196528, ECO:0000269|PubMed:1849459, ECO:0000269|PubMed:1850821, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:27676246, ECO:0000269|PubMed:8155326, ECO:0000269|PubMed:8325889}.; ","acmg|gedi|foundationOne|level2",{"$nulls":3},"p.Arg3Pro","c.8G>C","MODERATE","3/796",1,{"$nulls":5},"5","190","139","181","125","127","101","0","0","0","0.0792",{"$nulls":20},"2.848502","-1.05;-1.07;-1.08","0.805;0.805;.","1;0.921651;0.921651;0.921651","-0.65","0.001;0.001;.","0.094;0.079;0.072","0.388;0.324;0.398",{"$nulls":3},"Unknown",-1,"AR","Insensitivity to pain, congenital, with anhidrosis","Allergy/Immunology/Infectious; Neurologic","COSMIC,kAPOPTOSIS,kCANCER,kMAPK,vRTK",null,null,"C0020074","0/0","187,1","0.0053","188","0/1","127,9","0.0662","136",null,"chr1:156860942:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.064"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","NTRK1","chr1:156860942","NTRK1(R3P)",null,null,"signal peptide , splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Congenital insensitivity to pain with anhidrosis (CIPA) [MIM:256800]: Characterized by a congenital insensitivity to pain, anhidrosis (absence of sweating), absence of reaction to noxious stimuli, self-mutilating behavior, and mental retardation. This rare autosomal recessive disorder is also known as congenital sensory neuropathy with anhidrosis or hereditary sensory and autonomic neuropathy type IV or familial dysautonomia type II. {ECO:0000269|PubMed:10090906, ECO:0000269|PubMed:10233776, ECO:0000269|PubMed:10330344, ECO:0000269|PubMed:10567924, ECO:0000269|PubMed:10861667, ECO:0000269|PubMed:10982191, ECO:0000269|PubMed:11159935, ECO:0000269|PubMed:11310631, ECO:0000269|PubMed:18077166, ECO:0000269|PubMed:22302274, ECO:0000269|PubMed:27676246, ECO:0000269|PubMed:28177573, ECO:0000269|PubMed:28328124, ECO:0000269|PubMed:8696348}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Chromosomal aberrations involving NTRK1 are found in papillary thyroid carcinomas (PTCs) (PubMed:2869410, PubMed:7565764, PubMed:1532241). Translocation t(1;3)(q21;q11) with TFG generates the TRKT3 (TRK-T3) transcript by fusing TFG to the 3'-end of NTRK1 (PubMed:7565764). A rearrangement with TPM3 generates the TRK transcript by fusing TPM3 to the 3'-end of NTRK1 (PubMed:2869410). An intrachromosomal rearrangement that links the protein kinase domain of NTRK1 to the 5'-end of the TPR gene forms the fusion protein TRK-T1. TRK-T1 is a 55 kDa protein reacting with antibodies against the C-terminus of the NTRK1 protein (PubMed:1532241). {ECO:0000269|PubMed:1532241, ECO:0000269|PubMed:2869410, ECO:0000269|PubMed:7565764}.; ","FUNCTION: Receptor tyrosine kinase involved in the development and the maturation of the central and peripheral nervous systems through regulation of proliferation, differentiation and survival of sympathetic and nervous neurons. High affinity receptor for NGF which is its primary ligand (PubMed:1850821, PubMed:1849459, PubMed:1281417, PubMed:8325889, PubMed:15488758, PubMed:17196528, PubMed:27445338). Can also bind and be activated by NTF3/neurotrophin-3. However, NTF3 only supports axonal extension through NTRK1 but has no effect on neuron survival (By similarity). Upon dimeric NGF ligand-binding, undergoes homodimerization, autophosphorylation and activation (PubMed:1281417). Recruits, phosphorylates and/or activates several downstream effectors including SHC1, FRS2, SH2B1, SH2B2 and PLCG1 that regulate distinct overlapping signaling cascades driving cell survival and differentiation. Through SHC1 and FRS2 activates a GRB2-Ras-MAPK cascade that regulates cell differentiation and survival. Through PLCG1 controls NF-Kappa-B activation and the transcription of genes involved in cell survival. Through SHC1 and SH2B1 controls a Ras-PI3 kinase-AKT1 signaling cascade that is also regulating survival. In absence of ligand and activation, may promote cell death, making the survival of neurons dependent on trophic factors. {ECO:0000250|UniProtKB:P35739, ECO:0000250|UniProtKB:Q3UFB7, ECO:0000269|PubMed:11244088, ECO:0000269|PubMed:1281417, ECO:0000269|PubMed:15488758, ECO:0000269|PubMed:17196528, ECO:0000269|PubMed:1849459, ECO:0000269|PubMed:1850821, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:27676246, ECO:0000269|PubMed:8155326, ECO:0000269|PubMed:8325889}.; ","acmg|gedi|foundationOne|level2",{"$nulls":3},"p.Arg3Pro","c.8G>C","MODERATE","3/796",1,{"$nulls":5},"3","190","96",{"$nulls":4},"0","0",{"$nulls":22},"2.848502","-1.05;-1.07;-1.08","0.805;0.805;.","1;0.921651;0.921651;0.921651","-0.65","0.001;0.001;.","0.094;0.079;0.072","0.388;0.324;0.398",{"$nulls":3},"Unknown",-1,"AR","Insensitivity to pain, congenital, with anhidrosis","Allergy/Immunology/Infectious; Neurologic","COSMIC,kAPOPTOSIS,kCANCER,kMAPK,vRTK",null,null,"C0020074","0/0","187,1","0.0053","188","0/1","84,13","0.134","97",null,"chr1:156860942:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","NUP160","chr11:47840011","NUP160(D194N)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in poly(A)+ RNA transport. {ECO:0000269|PubMed:11684705}.; ",{"$nulls":4},"p.Asp194Asn","c.580G>A","MODERATE","194/1436",4,{"$nulls":5},"5","619","336","417","219","547","293","0","0","0","0.2014",{"$nulls":20},"2.148464","1.01","-0.345","1;1;0.944114;0.944114;0.944114","0.06","0.007","0.648","0.126",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748552","0/0","601,0","0","601","0/1","261,63","0.1944","324",null,"chr11:47840011:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1872"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","OR2A25","chr7:144074411","OR2A25(H64Q)",null,null,"transmembrane region (Helical; Name=2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.His64Gln","c.192C>G","MODERATE","64/310",1,{"$nulls":5},"4","1086","725","881","592","904","623","0","0","0","0.0658",{"$nulls":20},"1.722639",".;.;4.11","0.98","0.629249",".;.;-4.47","0.177",".;.;0.042",".;.;0.186",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","1075,0","0","1075","0/1","658,49","0.0693","707",null,"chr7:144074411:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0743"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","OR2C1","chr16:3356643","OR2C1(R235*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function","rs202058705",9.6979999999999994E-4,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Arg235*","c.703C>T","HIGH","235/312",1,1,{"$nulls":4},"5","833","469","710","389","698","400","0.0012","0.0012","0","0.0875",{"$nulls":20},"5.56394",null,null,"1",{"$nulls":3},"0.024",{"$nulls":3},"ExAC_SAS_AF",9.6979999999999994E-4,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","832,1","0.0012","833","0/1","416,40","0.0877","456",null,"chr16:3356643:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0874"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","OR2C1","chr16:3356643","OR2C1(R235*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function","rs202058705",9.6979999999999994E-4,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Arg235*","c.703C>T","HIGH","235/312",1,1,{"$nulls":4},"5","833","398","710","340","699","336","0.0012","0.0012","0","0.3006",{"$nulls":20},"5.56394",null,null,"1",{"$nulls":3},"0.024",{"$nulls":3},"ExAC_SAS_AF",9.6979999999999994E-4,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","834,1","0.0012","835","0/1","279,117","0.2955","396",null,"chr16:3356643:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3059"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","OR5T3","chr11:56253122","OR5T3(Y308C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Tyr308Cys","c.923A>G","MODERATE","308/340",1,{"$nulls":5},"4","584","341","437","237","499","274","0","0","0","0.1496",{"$nulls":20},"3.123524","8.12","3.09;.","0.887792","-8.42;-8.43","0.985;.","0.005;0.006","0.617;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","592,0","0","592","0/1","280,54","0.1617","334",null,"chr11:56253122:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1646"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","OR6F1","chr1:247712565","OR6F1(S64N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser64Asn","c.191G>A","MODERATE","64/308",1,{"$nulls":5},"5","776","550","578","376","704","502","0","0","0","0.0637",{"$nulls":20},"2.067597",".;.;5.34","2.055","1",".;.;-1.61","0.92",".;.;0.038",".;.;0.148",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","776,0","0","776","0/1","501,37","0.0688","538",null,"chr1:247712565:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0798"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","OR6F1","chr1:247712565","OR6F1(S64N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser64Asn","c.191G>A","MODERATE","64/308",1,{"$nulls":5},"5","776","617","578","437","703","553","0","0","0","0.2278",{"$nulls":20},"2.067597",".;.;5.34","2.055","1",".;.;-1.61","0.92",".;.;0.038",".;.;0.148",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","775,0","0","775","0/1","456,140","0.2349","596",null,"chr1:247712565:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.254"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","OR7D4","chr19:9213997","OR7D4(V281L)",null,null,"transmembrane region (Helical; Name=7 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. Selectively activated by androstenone and the related odorous steroid androstadienone.; ",{"$nulls":4},"p.Val281Leu","c.841G>C","MODERATE","281/312",1,{"$nulls":5},"4","573","425","435","308","490","366","0","0","0","0.1038",{"$nulls":20},"1.938734",".;.;8.5","2.075","0.87753",".;.;-2.57","0.863",".;.;0.001",".;.;0.067",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","566,0","0","566","0/1","361,39","0.0975","400",null,"chr19:9213997:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1006"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","OR7D4","chr19:9213997","OR7D4(V281L)",null,null,"transmembrane region (Helical; Name=7 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. Selectively activated by androstenone and the related odorous steroid androstadienone.; ",{"$nulls":4},"p.Val281Leu","c.841G>C","MODERATE","281/312",1,{"$nulls":5},"4","573","465","435","346","490","409","0","0","0","0.1834",{"$nulls":20},"1.938734",".;.;8.5","2.075","0.87753",".;.;-2.57","0.863",".;.;0.001",".;.;0.067",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","558,0","0","558","0/1","352,87","0.1982","439",null,"chr19:9213997:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1936"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","OTOR","chr20:16751112","OTOR(C127*)",null,null,"disulfide bond ",{"$nulls":3},255,"PASS","Loss Of Function","rs370100954",-1,{"$nulls":6},"p.Cys127*","c.381C>A","HIGH","127/128",4,{"$nulls":5},"3",null,null,"39","28",{"$nulls":26},"6.812937",null,null,"0.777212",{"$nulls":3},"0.14",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","48,0","0","48","0/1","27,3","0.1","30",null,"chr20:16751112:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1071"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","P2RX3","chr11:57369972","P2RX3(S390L)",{"$nulls":6},255,"PASS","Missense","rs143889563",5.3937432578209273E-4,null,"FUNCTION: Receptor for ATP that acts as a ligand-gated cation channel (PubMed:27626375). Plays a role in sensory perception. Required for normal perception of pain. Required for normal taste perception (By similarity). {ECO:0000250|UniProtKB:Q3UR32, ECO:0000269|PubMed:27626375}.; ",{"$nulls":4},"p.Ser390Leu","c.1169C>T","MODERATE","390/397",12,{"$nulls":5},"5","753","496","521","334","701","444","0","0","0","0.1351",{"$nulls":20},"3.6849629999999998",".;3.4",".;2.325","0.999738",".;-2.02",".;1.0",".;0.006","0.456;0.337",{"$nulls":3},"TWINSUK_AF",5.3937432578209273E-4,{"$nulls":4},"The product of this gene belongs to the family of purinoceptors for ATP. This receptor functions as a ligand-gated ion channel and may transduce ATP-evoked nociceptor activation. Mouse studies suggest that this receptor is important for peripheral pain responses, and also participates in pathways controlling urinary bladder volume reflexes. It is possible that the development of selective antagonists for this receptor may have a therapeutic potential in pain relief and in the treatment of disorders of urine storage. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","727,0","0","727","0/1","398,79","0.1656","477",null,"chr11:57369972:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1437"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PADI6","chr1:17398705","PADI6(R570H)",{"$nulls":6},255,"PASS","Missense","rs372730186",1.3440000000000001E-4,"DISEASE: Preimplantation embryonic lethality 2 (PREMBL2) [MIM:617234]: A rare cause of female primary infertility. In affected women, ovulation and fertilization proceed normally but embryos are arrested at early stages of development. Inheritance is autosomal recessive. {ECO:0000269|PubMed:27545678}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the deimination of arginine residues of proteins (By similarity). May be involved in cytoskeletal reorganization in the egg and early embryo (PubMed:27545678). {ECO:0000250, ECO:0000269|PubMed:27545678}.; ",{"$nulls":4},"p.Arg570His","c.1709G>A","MODERATE","570/694",15,{"$nulls":5},"5","315","201","288","164","112","79","0","0","0","0.2785",{"$nulls":20},"3.009358",{"$nulls":6},"0.44",{"$nulls":3},"ExAC_NFE_AF",1.3440000000000001E-4,{"$nulls":4},"This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. This protein may play a role in cytoskeletal reorganization in the egg and in early embryo development. [provided by RefSeq, Sep 2012].  ",null,"C4310659","0/0","304,0","0","304","0/1","154,37","0.1937","191",null,"chr1:17398705:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1768"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PCDHB13","chr5:141215765","PCDHB13(R548C)",null,null,"topological domain (Extracellular ), domain (Cadherin 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Arg548Cys","c.1642C>T","MODERATE","548/798",1,2,{"$nulls":4},"5","524","174","462","140","453","126","0","0","0","0.2222",{"$nulls":20},"2.326752","4.65","2.44","0.931121","-7.47","1.0",null,"0.219",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","529,0","0","529","0/1","130,40","0.2353","170",null,"chr5:141215765:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.2214"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PCSK5","chr9:76292239","PCSK5(P1050R)",null,null,"topological domain (Extracellular ), repeat (FU 9 ), region of interest (CRM (Cys-rich motif) ), splice variant (In isoform PC6A. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine endoprotease that processes various proproteins by cleavage at paired basic amino acids, recognizing the RXXX[KR]R consensus motif. Likely functions in the constitutive and regulated secretory pathways. Plays an essential role in pregnancy establishment by proteolytic activation of a number of important factors such as BMP2, CALD1 and alpha-integrins. {ECO:0000269|PubMed:19764806, ECO:0000269|PubMed:20555025, ECO:0000269|PubMed:22740495}.; ",{"$nulls":4},"p.Pro1050Arg","c.3149C>G","MODERATE","1050/1860",25,{"$nulls":5},"5","1136","733","827","503","797","534","0","0","0","0.1292",{"$nulls":20},"2.463869","1.51;1.5","1.47;.","0.999756","-3.54;-3.52",null,"0.182;0.439","0.776;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1046,0","0","1046","0/1","568,70","0.1097","638",null,"chr9:76292239:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0934"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PEAR1","chr1:156907618","PEAR1(S219fs)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: When overexpressed, reduces the number of both early and late non-adherent myeloid progenitor cells. {ECO:0000250}.; ",{"$nulls":4},"p.Ser219fs","c.654_669delGTCCTGTTCCCAGGGC","HIGH","218/1037",7,{"$nulls":5},"3",null,null,"679","391","874","516",null,null,"0","0.0872",{"$nulls":5},"(PEAR1|ENSG00000187800|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","1002,0","0","1002","0/1","499,52","0.0944","551",null,"chr1:156907618:TGTCCTGTTCCCAGGGC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0767"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PIP5KL1","chr9:127927674","PIP5KL1(P178R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a scaffold to localize and regulate type I PI(4)P 5-kinases to specific compartments within the cell, where they generate PI(4,5)P2 for actin nucleation, signaling and scaffold protein recruitment and conversion to PI(3,4,5)P3. {ECO:0000250}.; ",{"$nulls":4},"p.Pro178Arg","c.533C>G","MODERATE","178/394",5,{"$nulls":5},"5","215","88","171","69","164","69","0","0","0","0.1594",{"$nulls":20},"4.295013","1.37","3.035","1","-7.55","0.998",null,"0.665",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","213,0","0","213","0/1","74,13","0.1494","87",null,"chr9:127927674:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1304"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PPM1F","chr22:21933546","PPM1F(D198H)",null,null,"domain (PPM-type phosphatase ), metal ion-binding site (Manganese 1), metal ion-binding site (Manganese 2)","metal-binding-site:Manganese_1, metal-binding-site:Manganese_2","LOW, LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Dephosphorylates and concomitantly deactivates CaM- kinase II activated upon autophosphorylation, and CaM-kinases IV and I activated upon phosphorylation by CaM-kinase kinase. Promotes apoptosis.; ",{"$nulls":4},"p.Asp198His","c.592G>C","MODERATE","198/454",5,{"$nulls":5},"5","334","185","223","124","316","168","0","0","0","0.1429",{"$nulls":20},"4.086291","0.43","4.89;.;.;.","1","-7.0","1.0;.;1.0;.","0.0","0.969;0.977;0.964;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. This phosphatase can interact with Rho guanine nucleotide exchange factors (PIX), and thus block the effects of p21-activated kinase 1 (PAK), a protein kinase mediating biological effects downstream of Rho GTPases. Calcium/calmodulin-dependent protein kinase II gamma (CAMK2G/CAMK-II) is found to be one of the substrates of this phosphatase. The overexpression of this phosphatase or CAMK2G has been shown to mediate caspase-dependent apoptosis. An alternatively spliced transcript variant has been identified, but its full-length nature has not been determined. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","331,0","0","331","0/1","153,25","0.1404","178",null,"chr22:21933546:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1452"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PRDM16","chr1:3186392","PRDM16(R102K)",null,null,"domain (SET ), splice variant (In isoform 4. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cardiomyopathy, dilated 1LL (CMD1LL) [MIM:615373]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:23768516}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving PRDM16 is found in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Reciprocal translocation t(1;3)(p36;q21). Isoform 4 is specifically expressed in adult T-cell leukemia. {ECO:0000269|PubMed:11050005, ECO:0000269|PubMed:12557231}.; ","FUNCTION: Binds DNA and functions as a transcriptional regulator. Functions in the differentiation of brown adipose tissue (BAT) which is specialized in dissipating chemical energy in the form of heat in response to cold or excess feeding while white adipose tissue (WAT) is specialized in the storage of excess energy and the control of systemic metabolism. Together with CEBPB, regulates the differentiation of myoblastic precursors into brown adipose cells. Functions also as a repressor of TGF-beta signaling. Isoform 4 may regulate granulocytes differentiation. {ECO:0000269|PubMed:12816872, ECO:0000269|PubMed:14656887, ECO:0000269|PubMed:19049980}.; ","level2",{"$nulls":3},"p.Arg102Lys","c.305G>A","MODERATE","102/1276",2,{"$nulls":5},"5","498","176","361","139","455","159","0","0","0","0.2579",{"$nulls":20},"1.349599","-2.02;-0.65;-2.02;-0.65",".;-0.295;.;-0.295","0.999623","-0.12;-0.08;-0.12;-0.08",".;0.0;.;0.0","0.479;0.445;0.488;0.415","0.197;0.257;0.192;0.186",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, dilated, ILL; Left ventricular noncompaction 8","Cardiovascular","COSMIC",null,null,"C3809288","0/0","494,0","0","494","0/1","128,47","0.2686","175",null,"chr1:3186392:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2518"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","PRRC2C","chr1:171517639","PRRC2C(S192*)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ser192*","c.575C>G","HIGH","192/2819",6,{"$nulls":5},"4","247","119","218","113","203","95","0","0","0","0.0737",{"$nulls":5},"(PRRC2C|ENSG00000117523|1|1.00)","(PRRC2C|ENSG00000117523|1|1.00)",{"$nulls":13},"6.51349",null,null,"1",{"$nulls":3},"0.227;0.226;0.239",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","247,0","0","247","0/1","112,6","0.0508","118",null,"chr1:171517639:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0531"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PRRC2C","chr1:171517639","PRRC2C(S192*)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ser192*","c.575C>G","HIGH","192/2819",6,{"$nulls":5},"5","247","158","218","145","201","130","0","0","0","0.2154",{"$nulls":5},"(PRRC2C|ENSG00000117523|1|1.00)","(PRRC2C|ENSG00000117523|1|1.00)",{"$nulls":13},"6.51349",null,null,"1",{"$nulls":3},"0.227;0.226;0.239",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","247,0","0","247","0/1","127,29","0.1859","156",null,"chr1:171517639:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1862"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","PRTN3","chr19:847908","PRTN3(A237D)",null,null,"domain (Peptidase S1 ), helix ",{"$nulls":3},255,"PASS","Missense","rs749095091",1.361E-4,"DISEASE: Note=Is the major autoantigen in anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (Wegener's granulomatosis) (PubMed:2377228, PubMed:2679910). This complex, systemic disease is characterized by granulomatous inflammation with necrotizing lesions in the respiratory tract, glomerulonephritis, vasculitis, and anti-neutrophil cytoplasmatic autoantibodies detected in patient sera (PubMed:2377228, PubMed:2679910). PRTN3 causes emphysema when administered by tracheal insufflation to hamsters (PubMed:3198760). {ECO:0000269|PubMed:3198760, ECO:0000303|PubMed:2377228, ECO:0000303|PubMed:2679910}.; ","FUNCTION: Serine protease that degrades elastin, fibronectin, laminin, vitronectin, and collagen types I, III, and IV (in vitro) (PubMed:3198760, PubMed:2033050, PubMed:28240246). By cleaving and activating receptor F2RL1/PAR-2, enhances endothelial cell barrier function and thus vascular integrity during neutrophil transendothelial migration (PubMed:23202369). May play a role in neutrophil transendothelial migration, probably when associated with CD177 (PubMed:22266279). {ECO:0000269|PubMed:2033050, ECO:0000269|PubMed:22266279, ECO:0000269|PubMed:23202369, ECO:0000269|PubMed:28240246, ECO:0000269|PubMed:3198760}.; ",{"$nulls":4},"p.Ala237Asp","c.710C>A","MODERATE","237/256",5,{"$nulls":5},"3","1245","813","836","531",null,null,"0","0",{"$nulls":22},"3.113718","-2.43;.","2.165;.","1","-3.04;.","1.0;.","0.002;.","0.416;0.4",{"$nulls":3},"ExAC_AMR_AF",1.361E-4,{"$nulls":7},"0/0","1196,0","0","1196","0/1","672,73","0.098","745",null,"chr19:847908:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0772"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PRTN3","chr19:847908","PRTN3(A237D)",null,null,"domain (Peptidase S1 ), helix ",{"$nulls":3},255,"PASS","Missense","rs749095091",1.361E-4,"DISEASE: Note=Is the major autoantigen in anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (Wegener's granulomatosis) (PubMed:2377228, PubMed:2679910). This complex, systemic disease is characterized by granulomatous inflammation with necrotizing lesions in the respiratory tract, glomerulonephritis, vasculitis, and anti-neutrophil cytoplasmatic autoantibodies detected in patient sera (PubMed:2377228, PubMed:2679910). PRTN3 causes emphysema when administered by tracheal insufflation to hamsters (PubMed:3198760). {ECO:0000269|PubMed:3198760, ECO:0000303|PubMed:2377228, ECO:0000303|PubMed:2679910}.; ","FUNCTION: Serine protease that degrades elastin, fibronectin, laminin, vitronectin, and collagen types I, III, and IV (in vitro) (PubMed:3198760, PubMed:2033050, PubMed:28240246). By cleaving and activating receptor F2RL1/PAR-2, enhances endothelial cell barrier function and thus vascular integrity during neutrophil transendothelial migration (PubMed:23202369). May play a role in neutrophil transendothelial migration, probably when associated with CD177 (PubMed:22266279). {ECO:0000269|PubMed:2033050, ECO:0000269|PubMed:22266279, ECO:0000269|PubMed:23202369, ECO:0000269|PubMed:28240246, ECO:0000269|PubMed:3198760}.; ",{"$nulls":4},"p.Ala237Asp","c.710C>A","MODERATE","237/256",5,{"$nulls":5},"4","1245","518","836","351","502","210","0","0","0","0.4143",{"$nulls":20},"3.113718","-2.43;.","2.165;.","1","-3.04;.","1.0;.","0.002;.","0.416;0.4",{"$nulls":3},"ExAC_AMR_AF",1.361E-4,{"$nulls":7},"0/0","1199,0","0","1199","0/1","301,188","0.3845","489",null,"chr19:847908:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3818"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","PTAR1","chr9:69750789","PTAR1(N83S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asn83Ser","c.248A>G","MODERATE","83/402",2,{"$nulls":5},"5","502","270","424","223","387","198","0","0","0","0.0657",{"$nulls":20},"2.571083",null,"1.05","0.999961;1","-1.58","0.012","0.201","0.472",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","495,0","0","495","0/1","251,14","0.0528","265",null,"chr9:69750789:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0538"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PTAR1","chr9:69750789","PTAR1(N83S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asn83Ser","c.248A>G","MODERATE","83/402",2,{"$nulls":5},"5","502","310","424","254","387","240","0","0","0","0.3292",{"$nulls":20},"2.571083",null,"1.05","0.999961;1","-1.58","0.012","0.201","0.472",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","499,0","0","499","0/1","206,97","0.3201","303",null,"chr9:69750789:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2953"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PTPRK","chr6:128005189","PTPRK(H807Y)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulation of processes involving cell contact and adhesion such as growth control, tumor invasion, and metastasis. Negative regulator of EGFR signaling pathway. Forms complexes with beta-catenin and gamma-catenin/plakoglobin. Beta-catenin may be a substrate for the catalytic activity of PTPRK/PTP-kappa. {ECO:0000269|PubMed:19836242}.; ",{"$nulls":4},"p.His807Tyr","c.2419C>T","MODERATE","807/1472",16,{"$nulls":5},"5","705","567","463","368","632","494","0","0","0","0.1093",{"$nulls":20},"2.575948","3.15;3.14;3.15;3.16;3.15;3.16;2.95",".;.;.;.;1.735;.;.","0.999998;0.999997;0.999998;0.999997;0.999998;0.999997;0.999997","-1.69;-1.7;-1.69;-1.7;-1.69;-1.66;-2.14","0.886;.;0.934;.;0.818;.;.","1.0;1.0;1.0;1.0;1.0;0.263;1.0","0.857;0.92;0.841;0.914;0.885;0.896;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","693,0","0","693","0/1","477,72","0.1311","549",null,"chr6:128005189:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1304"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","PZP","chr12:9166038","PZP(Sequence Feature)",{"$nulls":3},"glycosylation-site:N-linked_(GlcNAc...)","MODERATE",null,255,"PASS","Sequence Feature",null,-1,null,"FUNCTION: Is able to inhibit all four classes of proteinases by a unique 'trapping' mechanism. This protein has a peptide stretch, called the 'bait region' which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein which traps the proteinase. The entrapped enzyme remains active against low molecular weight substrates (activity against high molecular weight substrates is greatly reduced). Following cleavage in the bait region a thioester bond is hydrolyzed and mediates the covalent binding of the protein to the proteinase.; ",{"$nulls":5},"c.2258+8_2258+13delACTTTA","MODERATE",null,18,{"$nulls":5},"5","304","388","267","343","278","348","0","0","0","0.1006",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","332,0","0","332","0/1","372,37","0.0905","409",null,"chr12:9166038:GTAAAGT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0904"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RAB11FIP1","chr8:37872178","RAB11FIP1(C875S)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 2 and isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: A Rab11 effector protein involved in the endosomal recycling process. Also involved in controlling membrane trafficking along the phagocytic pathway and in phagocytosis. {ECO:0000269|PubMed:11786538, ECO:0000269|PubMed:15181150, ECO:0000269|PubMed:15355514, ECO:0000269|PubMed:16920206}.; ",{"$nulls":4},"p.Cys875Ser","c.2624G>C","MODERATE","875/1283",4,{"$nulls":5},"5","824","431","679","356","696","357","0","0","0","0.1289",{"$nulls":20},"-0.40507","2.89","-0.205","1;0.999999;0.999999;0.999999","-0.18",null,"0.768","0.052",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","816,0","0","816","0/1","363,56","0.1337","419",null,"chr8:37872178:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1236"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","RASIP1","chr19:48729198","RASIP1(C523fs)",{"$nulls":6},57.9063,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Required for the proper formation of vascular structures that develop via both vasculogenesis and angiogenesis. Acts as a critical and vascular-specific regulator of GTPase signaling, cell architecture, and adhesion, which is essential for endothelial cell morphogenesis and blood vessel tubulogenesis. Regulates the activity of Rho GTPases in part by recruiting ARHGAP29 and suppressing RhoA signaling and dampening ROCK and MYH9 activities in endothelial cells (By similarity). May act as effector for Golgi-bound HRAS and other Ras-like proteins. May promote HRAS- mediated transformation. Negative regulator of amino acid starvation-induced autophagy. {ECO:0000250, ECO:0000269|PubMed:15031288, ECO:0000269|PubMed:22354037}.; ",{"$nulls":4},"p.Cys523fs","c.1568_1571delGCGG","HIGH","523/963",5,{"$nulls":5},"3",null,null,"391","229",{"$nulls":11},"(RASIP1|ENSG00000105538|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","440,0","0","440","0/1","239,13","0.0516","252",null,"chr19:48729198:GCCGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0524"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RASIP1","chr19:48729198","RASIP1(C523fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Required for the proper formation of vascular structures that develop via both vasculogenesis and angiogenesis. Acts as a critical and vascular-specific regulator of GTPase signaling, cell architecture, and adhesion, which is essential for endothelial cell morphogenesis and blood vessel tubulogenesis. Regulates the activity of Rho GTPases in part by recruiting ARHGAP29 and suppressing RhoA signaling and dampening ROCK and MYH9 activities in endothelial cells (By similarity). May act as effector for Golgi-bound HRAS and other Ras-like proteins. May promote HRAS- mediated transformation. Negative regulator of amino acid starvation-induced autophagy. {ECO:0000250, ECO:0000269|PubMed:15031288, ECO:0000269|PubMed:22354037}.; ",{"$nulls":4},"p.Cys523fs","c.1568_1571delGCGG","HIGH","523/963",5,{"$nulls":5},"5","526","229","391","181","440","197","0","0","0","0.2284",{"$nulls":5},"(RASIP1|ENSG00000105538|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","529,0","0","529","0/1","177,51","0.2237","228",null,"chr19:48729198:GCCGC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2265"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RB1","chr13:48362952","RB1(D286H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Childhood cancer retinoblastoma (RB) [MIM:180200]: Congenital malignant tumor that arises from the nuclear layers of the retina. It occurs in about 1:20'000 live births and represents about 2% of childhood malignancies. It is bilateral in about 30% of cases. Although most RB appear sporadically, about 20% are transmitted as an autosomal dominant trait with incomplete penetrance. The diagnosis is usually made before the age of 2 years when strabismus or a gray to yellow reflex from pupil ('cat eye') is investigated. {ECO:0000269|PubMed:10671068, ECO:0000269|PubMed:11524739, ECO:0000269|PubMed:1352883, ECO:0000269|PubMed:2594029, ECO:0000269|PubMed:7704558, ECO:0000269|PubMed:7795591, ECO:0000269|PubMed:7927327, ECO:0000269|PubMed:8346255, ECO:0000269|PubMed:8605116, ECO:0000269|PubMed:8776589, ECO:0000269|PubMed:9140452, ECO:0000269|PubMed:9311732, ECO:0000269|PubMed:9973307}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Osteogenic sarcoma (OSRC) [MIM:259500]: A sarcoma originating in bone-forming cells, affecting the ends of long bones. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key regulator of entry into cell division that acts as a tumor suppressor. Promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. Acts as a transcription repressor of E2F1 target genes. The underphosphorylated, active form of RB1 interacts with E2F1 and represses its transcription activity, leading to cell cycle arrest. Directly involved in heterochromatin formation by maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin by stabilizing histone methylation. Recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. Controls histone H4 'Lys-20' trimethylation. Inhibits the intrinsic kinase activity of TAF1. Mediates transcriptional repression by SMARCA4/BRG1 by recruiting a histone deacetylase (HDAC) complex to the c-FOS promoter. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex (By similarity). In case of viral infections, interactions with SV40 large T antigen, HPV E7 protein or adenovirus E1A protein induce the disassembly of RB1-E2F1 complex thereby disrupting RB1's activity. {ECO:0000250, ECO:0000269|PubMed:15084261}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Palbociclib\" , \"Palbociclib\"]","[ \"Palbociclib\" , \"Palbociclib\"]","[ \"Palbociclib\" , \"Palbociclib\"]","p.Asp286His","c.856G>C","MODERATE","286/928",8,{"$nulls":5},"5","87","30","64","23","85","26","0","0","0","0.3462",{"$nulls":20},"3.960384","-3.0;.","1.955;.","0.999999","-2.68;.","1.0;.","0.042;.","0.455;.",{"$nulls":3},"Unknown",-1,"AD","Retinoblastoma","Oncologic","COSMIC,kCANCER,kCELL_CYCLE,vRB",null,null,"C0029463| C0035335| C0005684| C0149925| C0149925","0/0","87,0","0","87","0/1","20,10","0.3333","30",null,"chr13:48362952:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3478"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","RELN","chr7:103553552","RELN(S1994*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lissencephaly 2 (LIS2) [MIM:257320]: A classic type lissencephaly associated with ataxia, mental retardation, seizures and abnormalities of the cerebellum, hippocampus and brainstem. {ECO:0000269|PubMed:10973257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epilepsy, familial temporal lobe, 7 (ETL7) [MIM:616436]: A focal form of epilepsy characterized by recurrent seizures that arise from foci within the temporal lobe. Seizures are usually accompanied by sensory symptoms, most often auditory in nature. {ECO:0000269|PubMed:26046367}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Extracellular matrix serine protease that plays a role in layering of neurons in the cerebral cortex and cerebellum. Regulates microtubule function in neurons and neuronal migration. Affects migration of sympathetic preganglionic neurons in the spinal cord, where it seems to act as a barrier to neuronal migration. Enzymatic activity is important for the modulation of cell adhesion. Binding to the extracellular domains of lipoprotein receptors VLDLR and LRP8/APOER2 induces tyrosine phosphorylation of DAB1 and modulation of TAU phosphorylation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ser1994*","c.5981C>G","HIGH","1994/3460",40,{"$nulls":5},"5","572","337","433","247","479","284","0","0","0","0.081",{"$nulls":5},"(RELN|ENSG00000189056|1|1.00)","(RELN|ENSG00000189056|1|1.00)",{"$nulls":13},"9.337101",null,null,"1",{"$nulls":3},"0.953;0.953;0.954",{"$nulls":3},"Unknown",-1,"AR","Lissencephaly 2","Craniofacial; Neurologic",{"$nulls":3},"C4551957| C0796089| C4225327","0/0","568,0","0","568","0/1","304,23","0.0703","327",null,"chr7:103553552:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0729"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RELN","chr7:103553552","RELN(S1994*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lissencephaly 2 (LIS2) [MIM:257320]: A classic type lissencephaly associated with ataxia, mental retardation, seizures and abnormalities of the cerebellum, hippocampus and brainstem. {ECO:0000269|PubMed:10973257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epilepsy, familial temporal lobe, 7 (ETL7) [MIM:616436]: A focal form of epilepsy characterized by recurrent seizures that arise from foci within the temporal lobe. Seizures are usually accompanied by sensory symptoms, most often auditory in nature. {ECO:0000269|PubMed:26046367}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Extracellular matrix serine protease that plays a role in layering of neurons in the cerebral cortex and cerebellum. Regulates microtubule function in neurons and neuronal migration. Affects migration of sympathetic preganglionic neurons in the spinal cord, where it seems to act as a barrier to neuronal migration. Enzymatic activity is important for the modulation of cell adhesion. Binding to the extracellular domains of lipoprotein receptors VLDLR and LRP8/APOER2 induces tyrosine phosphorylation of DAB1 and modulation of TAU phosphorylation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ser1994*","c.5981C>G","HIGH","1994/3460",40,{"$nulls":5},"5","572","333","433","254","478","263","0","0","0","0.3346",{"$nulls":5},"(RELN|ENSG00000189056|1|1.00)","(RELN|ENSG00000189056|1|1.00)",{"$nulls":13},"9.337101",null,null,"1",{"$nulls":3},"0.953;0.953;0.954",{"$nulls":3},"Unknown",-1,"AR","Lissencephaly 2","Craniofacial; Neurologic",{"$nulls":3},"C4551957| C0796089| C4225327","0/0","567,0","0","567","0/1","223,99","0.3075","322",null,"chr7:103553552:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.311"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RLF","chr1:40240064","RLF(D1788N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp1788Asn","c.5362G>A","MODERATE","1788/1914",8,{"$nulls":5},"4","495","271","415","232","254","143","0","0","0","0.2517",{"$nulls":20},"2.899336","2.49","1.445","0.997678","-0.52","0.987","0.26","0.336",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","502,0","0","502","0/1","228,43","0.1587","271",null,"chr1:40240064:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1595"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ROCK2","chr2:11192217","ROCK2(T1365I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Protein kinase which is a key regulator of actin cytoskeleton and cell polarity. Involved in regulation of smooth muscle contraction, actin cytoskeleton organization, stress fiber and focal adhesion formation, neurite retraction, cell adhesion and motility via phosphorylation of ADD1, BRCA2, CNN1, EZR, DPYSL2, EP300, MSN, MYL9/MLC2, NPM1, RDX, PPP1R12A and VIM. Phosphorylates SORL1 and IRF4. Acts as a negative regulator of VEGF-induced angiogenic endothelial cell activation. Positively regulates the activation of p42/MAPK1-p44/MAPK3 and of p90RSK/RPS6KA1 during myogenic differentiation. Plays an important role in the timely initiation of centrosome duplication. Inhibits keratinocyte terminal differentiation. May regulate closure of the eyelids and ventral body wall through organization of actomyosin bundles. Plays a critical role in the regulation of spine and synaptic properties in the hippocampus. Plays an important role in generating the circadian rhythm of the aortic myofilament Ca(2+) sensitivity and vascular contractility by modulating the myosin light chain phosphorylation. {ECO:0000269|PubMed:10579722, ECO:0000269|PubMed:15699075, ECO:0000269|PubMed:16574662, ECO:0000269|PubMed:17015463, ECO:0000269|PubMed:19131646, ECO:0000269|PubMed:19997641, ECO:0000269|PubMed:21084279, ECO:0000269|PubMed:21147781}.; ","level2",{"$nulls":3},"p.Thr1365Ile","c.4094C>T","MODERATE","1365/1388",32,{"$nulls":5},"5","407","244","296","172","328","208","0","0","0","0.1442",{"$nulls":20},"3.317951","-0.02;.;1.04","0;.;.","0.994295;0.982998","-1.55;.;-1.44","0.263;.;.","0.131;.;0.133","0.357;0.384;0.347",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kTGF_BETA,kWNT",{"$nulls":3},"0/0","397,0","0","397","0/1","208,30","0.1261","238",null,"chr2:11192217:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1163"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ROCK2","chr2:11192217","ROCK2(T1365I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Protein kinase which is a key regulator of actin cytoskeleton and cell polarity. Involved in regulation of smooth muscle contraction, actin cytoskeleton organization, stress fiber and focal adhesion formation, neurite retraction, cell adhesion and motility via phosphorylation of ADD1, BRCA2, CNN1, EZR, DPYSL2, EP300, MSN, MYL9/MLC2, NPM1, RDX, PPP1R12A and VIM. Phosphorylates SORL1 and IRF4. Acts as a negative regulator of VEGF-induced angiogenic endothelial cell activation. Positively regulates the activation of p42/MAPK1-p44/MAPK3 and of p90RSK/RPS6KA1 during myogenic differentiation. Plays an important role in the timely initiation of centrosome duplication. Inhibits keratinocyte terminal differentiation. May regulate closure of the eyelids and ventral body wall through organization of actomyosin bundles. Plays a critical role in the regulation of spine and synaptic properties in the hippocampus. Plays an important role in generating the circadian rhythm of the aortic myofilament Ca(2+) sensitivity and vascular contractility by modulating the myosin light chain phosphorylation. {ECO:0000269|PubMed:10579722, ECO:0000269|PubMed:15699075, ECO:0000269|PubMed:16574662, ECO:0000269|PubMed:17015463, ECO:0000269|PubMed:19131646, ECO:0000269|PubMed:19997641, ECO:0000269|PubMed:21084279, ECO:0000269|PubMed:21147781}.; ","level2",{"$nulls":3},"p.Thr1365Ile","c.4094C>T","MODERATE","1365/1388",32,{"$nulls":5},"5","407","251","296","171","326","208","0","0","0","0.4856",{"$nulls":20},"3.317951","-0.02;.;1.04","0;.;.","0.994295;0.982998","-1.55;.;-1.44","0.263;.;.","0.131;.;0.133","0.357;0.384;0.347",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kTGF_BETA,kWNT",{"$nulls":3},"0/0","397,0","0","397","0/1","139,108","0.4372","247",null,"chr2:11192217:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3977"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","RPP38","chr10:15103838","RPP38(K175T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. RPP38 may associate transiently with RNase P RNA as a factor involved in the transport of H1 RNA to the putative site of its assembly in the cell, the nucleolus.; ",{"$nulls":4},"p.Lys175Thr","c.524A>C","MODERATE","175/283",3,{"$nulls":5},"4","852","517","650","393",null,null,"0","0",{"$nulls":22},"2.183895","0.26;.;0.26;0.26","1.955","0.985691;0.985691;0.985691;1","-2.42;.;-2.42;-2.42","0.17","0.155;.;0.155;0.155","0.203;0.203;0.202;0.202",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","849,0","0","849","0/1","478,26","0.0516","504",null,"chr10:15103838:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0509"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RPP38","chr10:15103838","RPP38(K175T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. RPP38 may associate transiently with RNase P RNA as a factor involved in the transport of H1 RNA to the putative site of its assembly in the cell, the nucleolus.; ",{"$nulls":4},"p.Lys175Thr","c.524A>C","MODERATE","175/283",3,{"$nulls":5},"5","852","606","650","459","735","504","0","0","0","0.119",{"$nulls":20},"2.183895","0.26;.;0.26;0.26","1.955","0.985691;0.985691;0.985691;1","-2.42;.;-2.42;-2.42","0.17","0.155;.;0.155;0.155","0.203;0.203;0.202;0.202",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","854,0","0","854","0/1","517,71","0.1207","588",null,"chr10:15103838:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1198"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","RSF1","chr11:77683820","RSF1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Required for assembly of regular nucleosome arrays by the RSF chromatin-remodeling complex (PubMed:12972596). Facilitates transcription of hepatitis B virus (HBV) genes by the pX transcription activator. In case of infection by HBV, together with pX, it represses TNF-alpha induced NF-kappa-B transcription activation. Represses transcription when artificially recruited to chromatin by fusion to a heterogeneous DNA binding domain (PubMed:11944984, PubMed:11788598). {ECO:0000269|PubMed:11788598, ECO:0000269|PubMed:11944984, ECO:0000269|PubMed:12972596}.; ",{"$nulls":5},"c.2956-2dupA","HIGH",null,10,{"$nulls":5},"4","127","56","90","46",null,null,"0","0",{"$nulls":7},"(RSF1|ENSG00000048649|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","122,0","0","122","0/1","48,5","0.0943","53",null,"chr11:77683820:C:CT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0652"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RSF1","chr11:77683820","RSF1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Required for assembly of regular nucleosome arrays by the RSF chromatin-remodeling complex (PubMed:12972596). Facilitates transcription of hepatitis B virus (HBV) genes by the pX transcription activator. In case of infection by HBV, together with pX, it represses TNF-alpha induced NF-kappa-B transcription activation. Represses transcription when artificially recruited to chromatin by fusion to a heterogeneous DNA binding domain (PubMed:11944984, PubMed:11788598). {ECO:0000269|PubMed:11788598, ECO:0000269|PubMed:11944984, ECO:0000269|PubMed:12972596}.; ",{"$nulls":5},"c.2956-2dupA","HIGH",null,10,{"$nulls":5},"4","127","56","90","38",null,null,"0","0",{"$nulls":7},"(RSF1|ENSG00000048649|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","122,0","0","122","0/1","34,15","0.3061","49",null,"chr11:77683820:C:CT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2368"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","RYR2","chr1:237614844","RYR2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Arrhythmogenic right ventricular dysplasia, familial, 2 (ARVD2) [MIM:600996]: A congenital heart disease characterized by infiltration of adipose and fibrous tissue into the right ventricle and loss of myocardial cells, resulting in ventricular and supraventricular arrhythmias. {ECO:0000269|PubMed:11159936}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ventricular tachycardia, catecholaminergic polymorphic, 1, with or without atrial dysfunction and/or dilated cardiomyopathy (CPVT1) [MIM:604772]: An arrhythmogenic disorder characterized by stress-induced, bidirectional ventricular tachycardia that may degenerate into cardiac arrest and cause sudden death. Patients present with recurrent syncope, seizures, or sudden death after physical activity or emotional stress. CPVT1 inheritance is autosomal dominant. {ECO:0000269|PubMed:11157710, ECO:0000269|PubMed:11208676, ECO:0000269|PubMed:12093772, ECO:0000269|PubMed:12106942, ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:15046072, ECO:0000269|PubMed:15046073, ECO:0000269|PubMed:15466642, ECO:0000269|PubMed:15544015, ECO:0000269|PubMed:16188589, ECO:0000269|PubMed:17984046, ECO:0000269|PubMed:24793461, ECO:0000269|PubMed:25372681, ECO:0000269|PubMed:27733687}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering cardiac muscle contraction. Aberrant channel activation can lead to cardiac arrhythmia. In cardiac myocytes, calcium release is triggered by increased Ca(2+) levels due to activation of the L-type calcium channel CACNA1C. The calcium channel activity is modulated by formation of heterotetramers with RYR3. Required for cellular calcium ion homeostasis. Required for embryonic heart development. {ECO:0000269|PubMed:10830164, ECO:0000269|PubMed:20056922, ECO:0000269|PubMed:27733687}.; ","acmg",{"$nulls":4},"c.5715+1G>A","HIGH",null,37,{"$nulls":5},"5","359","212","270","167","331","181","0","0","0","0.0663",{"$nulls":5},"(RYR2|ENSG00000198626|1|1.00)",{"$nulls":14},"6.091349",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Ventricular tachycardia, catecholaminergic polymorphic, 1; Arrhythmogenic right ventricular dysplasia 2  ","Cardiovascular",null,"This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008].  ",null,"C1832931| C4053736","0/0","365,0","0","365","0/1","198,15","0.0704","213",null,"chr1:237614844:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0659"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","RYR2","chr1:237614844","RYR2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Arrhythmogenic right ventricular dysplasia, familial, 2 (ARVD2) [MIM:600996]: A congenital heart disease characterized by infiltration of adipose and fibrous tissue into the right ventricle and loss of myocardial cells, resulting in ventricular and supraventricular arrhythmias. {ECO:0000269|PubMed:11159936}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ventricular tachycardia, catecholaminergic polymorphic, 1, with or without atrial dysfunction and/or dilated cardiomyopathy (CPVT1) [MIM:604772]: An arrhythmogenic disorder characterized by stress-induced, bidirectional ventricular tachycardia that may degenerate into cardiac arrest and cause sudden death. Patients present with recurrent syncope, seizures, or sudden death after physical activity or emotional stress. CPVT1 inheritance is autosomal dominant. {ECO:0000269|PubMed:11157710, ECO:0000269|PubMed:11208676, ECO:0000269|PubMed:12093772, ECO:0000269|PubMed:12106942, ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:15046072, ECO:0000269|PubMed:15046073, ECO:0000269|PubMed:15466642, ECO:0000269|PubMed:15544015, ECO:0000269|PubMed:16188589, ECO:0000269|PubMed:17984046, ECO:0000269|PubMed:24793461, ECO:0000269|PubMed:25372681, ECO:0000269|PubMed:27733687}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering cardiac muscle contraction. Aberrant channel activation can lead to cardiac arrhythmia. In cardiac myocytes, calcium release is triggered by increased Ca(2+) levels due to activation of the L-type calcium channel CACNA1C. The calcium channel activity is modulated by formation of heterotetramers with RYR3. Required for cellular calcium ion homeostasis. Required for embryonic heart development. {ECO:0000269|PubMed:10830164, ECO:0000269|PubMed:20056922, ECO:0000269|PubMed:27733687}.; ","acmg",{"$nulls":4},"c.5715+1G>A","HIGH",null,37,{"$nulls":5},"5","359","257","270","182","329","223","0","0","0","0.3901",{"$nulls":5},"(RYR2|ENSG00000198626|1|1.00)",{"$nulls":14},"6.091349",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Ventricular tachycardia, catecholaminergic polymorphic, 1; Arrhythmogenic right ventricular dysplasia 2  ","Cardiovascular",null,"This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008].  ",null,"C1832931| C4053736","0/0","365,0","0","365","0/1","154,101","0.3961","255",null,"chr1:237614844:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4066"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SETDB1","chr1:150959280","SETDB1(Q811H)",null,null,"domain (SET ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). {ECO:0000269|PubMed:12869583, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.; ","gedi",{"$nulls":3},"p.Gln811His","c.2433G>C","MODERATE","811/1291",15,{"$nulls":5},"4","691","452","481","308","618","397","0","0","0","0.0907",{"$nulls":20},"3.4362019999999998","-2.46","1.825;1.825;.","0.999984","-1.92","0.996;0.998;0.998","0.2;0.199;0.131","0.43;0.404;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","662,0","0","662","0/1","379,42","0.0998","421",null,"chr1:150959280:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0974"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SETDB1","chr1:150959280","SETDB1(Q811H)",null,null,"domain (SET ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). {ECO:0000269|PubMed:12869583, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.; ","gedi",{"$nulls":3},"p.Gln811His","c.2433G>C","MODERATE","811/1291",15,{"$nulls":5},"4","691","453","481","301","622","388","0","0","0","0.2216",{"$nulls":20},"3.4362019999999998","-2.46","1.825;1.825;.","0.999984","-1.92","0.996;0.998;0.998","0.2;0.199;0.131","0.43;0.404;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","662,0","0","662","0/1","330,89","0.2124","419",null,"chr1:150959280:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2126"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SETDB1","chr1:150964284","SETDB1(Y1267del)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). {ECO:0000269|PubMed:12869583, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.; ","gedi",{"$nulls":3},"p.Tyr1267del","c.3799_3801delTAC","MODERATE","1267/1291",22,{"$nulls":5},"4","925","675","745","524","809","577","0","0","0","0.1109",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","903,0","0","903","0/1","562,76","0.1191","638",null,"chr1:150964284:AACT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1298"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SETDB1","chr1:150964284","SETDB1(Y1267del)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). {ECO:0000269|PubMed:12869583, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.; ","gedi",{"$nulls":3},"p.Tyr1267del","c.3799_3801delTAC","MODERATE","1267/1291",22,{"$nulls":5},"4","925","665","745","502","811","591","0","0","0","0.3875",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","905,0","0","905","0/1","379,260","0.4069","639",null,"chr1:150964284:AACT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3506"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SF3B2","chr11:66053027","SF3B2(T61S)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077). {ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643}.; ",{"$nulls":4},"p.Thr61Ser","c.181A>T","MODERATE","61/895",3,{"$nulls":5},"3","1064","679",null,null,"851","532","0","0","0","0.0677",{"$nulls":20},"3.792593",null,".;1.955;.;.;.","0.943827","-0.78;-0.64;-2.73;-2.7;-2.36",".;0.037;.;0.012;.","0.0;0.0;0.022;0.022;0.021","0.453;0.409;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1030,0","0","1030","0/1","601,36","0.0565","637",null,"chr11:66053027:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SF3B2","chr11:66053027","SF3B2(T61S)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077). {ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643}.; ",{"$nulls":4},"p.Thr61Ser","c.181A>T","MODERATE","61/895",3,{"$nulls":5},"4","1064","587","791","419","855","465","0","0","0","0.1484",{"$nulls":20},"3.792593",null,".;1.955;.;.;.","0.943827","-0.78;-0.64;-2.73;-2.7;-2.36",".;0.037;.;0.012;.","0.0;0.0;0.022;0.022;0.021","0.453;0.409;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1031,0","0","1031","0/1","483,81","0.1436","564",null,"chr11:66053027:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1337"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SH2D2A","chr1:156815036","SH2D2A(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Could be a T-cell-specific adapter protein involved in the control of T-cell activation. May play a role in the CD4-p56- LCK-dependent signal transduction pathway. Could also play an important role in normal and pathological angiogenesis. Could be an adapter protein that facilitates and regulates interaction of KDR with effector proteins important to endothelial cell survival and proliferation.; ","level2",{"$nulls":4},"c.308+1G>T","HIGH",null,3,{"$nulls":5},"3",null,null,"198","111",{"$nulls":11},"(SH2D2A|ENSG00000027869|1|1.00)",{"$nulls":14},"5.783559",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":3},"kVEGF",{"$nulls":3},"0/0","204,0","0","204","0/1","110,6","0.0517","116",null,"chr1:156815036:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0631"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SH2D2A","chr1:156815036","SH2D2A(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Could be a T-cell-specific adapter protein involved in the control of T-cell activation. May play a role in the CD4-p56- LCK-dependent signal transduction pathway. Could also play an important role in normal and pathological angiogenesis. Could be an adapter protein that facilitates and regulates interaction of KDR with effector proteins important to endothelial cell survival and proliferation.; ","level2",{"$nulls":4},"c.308+1G>T","HIGH",null,3,{"$nulls":5},"5","204","109","198","101","139","70","0","0","0","0.2",{"$nulls":5},"(SH2D2A|ENSG00000027869|1|1.00)",{"$nulls":14},"5.783559",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":3},"kVEGF",{"$nulls":3},"0/0","207,0","0","207","0/1","91,16","0.1495","107",null,"chr1:156815036:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1287"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SIGLEC12","chr19:51499675","SIGLEC12(E284Q)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.; ",{"$nulls":4},"p.Glu284Gln","c.850G>C","MODERATE","284/595",3,{"$nulls":5},"5","966","597","710","429","868","542","0","0","0","0.059",{"$nulls":20},"1.303126","3.73","2.63;.","1","-2.15;.","0.91;0.662","0.021;.","0.042;0.04",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","949,0","0","949","0/1","532,39","0.0683","571",null,"chr19:51499675:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0583"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SIGLEC12","chr19:51499675","SIGLEC12(E284Q)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.; ",{"$nulls":4},"p.Glu284Gln","c.850G>C","MODERATE","284/595",3,{"$nulls":5},"5","966","395","710","261","870","346","0","0","0","0.3728",{"$nulls":20},"1.303126","3.73","2.63;.","1","-2.15;.","0.91;0.662","0.021;.","0.042;0.04",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","949,0","0","949","0/1","241,145","0.3756","386",null,"chr19:51499675:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3716"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SKOR2","chr18:47219981","SKOR2(L983I)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Exhibits transcriptional repressor activity (By similarity). Acts as a TGF-beta antagonist in the nervous system. {ECO:0000250, ECO:0000269|PubMed:16200078}.; ",{"$nulls":4},"p.Leu983Ile","c.2947C>A","MODERATE","983/1015",7,{"$nulls":5},"5","606","256","410","174","545","221","0.0017","0.0017","0","0.1312",{"$nulls":20},"2.966335","-0.27;.",null,"0.837239","-1.75;.",null,"0.0;.","0.409;0.42",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","574,1","0.0017","575","0/1","207,34","0.1411","241",null,"chr18:47219981:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1437"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SLC12A8","chr3:125107854","SLC12A8(Y441_E444delinsTer)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Cation/chloride cotransporter that may play a role in the control of keratinocyte proliferation. {ECO:0000269|PubMed:11863360}.; ",{"$nulls":4},"p.Tyr441_Glu444delinsTer","c.1323_1331delCGGCTCTGA","HIGH","441/714",9,{"$nulls":5},"4",null,null,"725","426","791","502",null,null,"0","0.0737",{"$nulls":5},"(SLC12A8|ENSG00000221955|1|1.00)","(SLC12A8|ENSG00000221955|1|1.00)",{"$nulls":24},"Unknown",-1,{"$nulls":7},"0/0","961,0","0","961","0/1","529,42","0.0736","571",null,"chr3:125107854:CTCAGAGCCG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0845"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SLC12A8","chr3:125107854","SLC12A8(Y441_E444delinsTer)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Cation/chloride cotransporter that may play a role in the control of keratinocyte proliferation. {ECO:0000269|PubMed:11863360}.; ",{"$nulls":4},"p.Tyr441_Glu444delinsTer","c.1323_1331delCGGCTCTGA","HIGH","441/714",9,{"$nulls":5},"5","920","398","725","306","791","346","0","0","0","0.3844",{"$nulls":5},"(SLC12A8|ENSG00000221955|1|1.00)","(SLC12A8|ENSG00000221955|1|1.00)",{"$nulls":24},"Unknown",-1,{"$nulls":7},"0/0","959,0","0","959","0/1","245,130","0.3467","375",null,"chr3:125107854:CTCAGAGCCG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3562"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SLC32A1","chr20:38728052","SLC32A1(Q331*)",null,null,"topological domain (Lumenal, vesicle )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Involved in the uptake of GABA and glycine into the synaptic vesicles. {ECO:0000250|UniProtKB:O35458}.; ",{"$nulls":4},"p.Gln331*","c.991C>T","HIGH","331/525",2,{"$nulls":5},"4","1280","726","996","529","1173","647","0","0","0","0.0912",{"$nulls":20},"7.382059",null,null,"1",{"$nulls":3},"0.896",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1276,0","0","1276","0/1","639,69","0.0975","708",null,"chr20:38728052:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0926"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SLC32A1","chr20:38728052","SLC32A1(Q331*)",null,null,"topological domain (Lumenal, vesicle )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Involved in the uptake of GABA and glycine into the synaptic vesicles. {ECO:0000250|UniProtKB:O35458}.; ",{"$nulls":4},"p.Gln331*","c.991C>T","HIGH","331/525",2,{"$nulls":5},"4","1280","561","996","416","1172","491","0","0","0","0.3951",{"$nulls":20},"7.382059",null,null,"1",{"$nulls":3},"0.896",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1281,0","0","1281","0/1","327,230","0.4129","557",null,"chr20:38728052:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4062"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SLC35C1","chr11:45810958","SLC35C1(I240F)",null,null,"transmembrane region (Helical ), sequence variant (In dbSNP:rs7130656. SLC35C1(I240V))",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Congenital disorder of glycosylation 2C (CDG2C) [MIM:266265]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. The clinical features of CDG2C include mental retardation, short stature, facial stigmata, and recurrent bacterial peripheral infections with persistently elevated peripheral leukocytes. Biochemically, CDG2C is characterized by a lack of fucosylated glycoconjugates, including selectin ligands. {ECO:0000269|PubMed:11326279, ECO:0000269|PubMed:11326280}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in GDP-fucose import from the cytoplasm into the Golgi lumen.; ",{"$nulls":4},"p.Ile240Phe","c.718A>T","MODERATE","240/364",2,{"$nulls":5},"5","1200","733","949","579","988","600","0","0","0","0.085",{"$nulls":20},"0.67717","-0.25",".;0.655","0.999978","-2.02",".;0.001","0.283;0.275","0.107;0.075",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type IIc; Leukocyte adhesion deficiency, type II","Allergy/Immunology/Infectious; Biochemical; Neurologic",{"$nulls":3},"C0398739","0/0","1170,0","0","1170","0/1","642,62","0.0881","704",null,"chr11:45810958:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0881"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SLC35C1","chr11:45810958","SLC35C1(I240F)",null,null,"transmembrane region (Helical ), sequence variant (In dbSNP:rs7130656. SLC35C1(I240V))",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Congenital disorder of glycosylation 2C (CDG2C) [MIM:266265]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. The clinical features of CDG2C include mental retardation, short stature, facial stigmata, and recurrent bacterial peripheral infections with persistently elevated peripheral leukocytes. Biochemically, CDG2C is characterized by a lack of fucosylated glycoconjugates, including selectin ligands. {ECO:0000269|PubMed:11326279, ECO:0000269|PubMed:11326280}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in GDP-fucose import from the cytoplasm into the Golgi lumen.; ",{"$nulls":4},"p.Ile240Phe","c.718A>T","MODERATE","240/364",2,{"$nulls":5},"5","1200","526","949","424","991","422","0","0","0","0.4218",{"$nulls":20},"0.67717","-0.25",".;0.655","0.999978","-2.02",".;0.001","0.283;0.275","0.107;0.075",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type IIc; Leukocyte adhesion deficiency, type II","Allergy/Immunology/Infectious; Biochemical; Neurologic",{"$nulls":3},"C0398739","0/0","1170,0","0","1170","0/1","297,214","0.4188","511",null,"chr11:45810958:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4363"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SLC38A9","chr5:55664707","SLC38A9(G228A)",null,null,"topological domain (Lumenal )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Lysosomal amino acid transporter involved in the activation of mTORC1 in response to amino acids. Probably acts as an amino acid sensor of the Rag GTPases and Ragulator complexes, 2 complexes involved in amino acid sensing and activation of mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels, and amino acids (PubMed:25561175, PubMed:25567906). Following activation by amino acids, the Ragulator and Rag GTPases function as a scaffold recruiting mTORC1 to lysosomes where it is in turn activated. SLC38A9 mediates transport of amino acids with low capacity and specificity with a slight preference for polar amino acids, suggesting that it acts as an amino acid sensor instead (PubMed:25561175, PubMed:25567906). The high concentration of arginine in lysosomes suggests that it acts as an arginine sensor (PubMed:25567906). {ECO:0000269|PubMed:25561175, ECO:0000269|PubMed:25567906}.; ",{"$nulls":4},"p.Gly228Ala","c.683G>C","MODERATE","228/561",6,{"$nulls":5},"5","113","61","98","49","74","40","0","0","0","0.175",{"$nulls":20},"3.275822","4.42","2.65;.;2.65;.;.;.;.","1","-1.91;-1.51;-1.91;-1.51;-1.58;-1.85;-2.77","1.0;.;1.0;.;.;.;.","0.159;1.0;0.159;0.726;0.136;0.604;1.0","0.705;0.766;0.706;0.712;0.694;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","111,0","0","111","0/1","51,8","0.1356","59",null,"chr5:55664707:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1429"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SLC38A9","chr5:55664707","SLC38A9(G228A)",null,null,"topological domain (Lumenal )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Lysosomal amino acid transporter involved in the activation of mTORC1 in response to amino acids. Probably acts as an amino acid sensor of the Rag GTPases and Ragulator complexes, 2 complexes involved in amino acid sensing and activation of mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels, and amino acids (PubMed:25561175, PubMed:25567906). Following activation by amino acids, the Ragulator and Rag GTPases function as a scaffold recruiting mTORC1 to lysosomes where it is in turn activated. SLC38A9 mediates transport of amino acids with low capacity and specificity with a slight preference for polar amino acids, suggesting that it acts as an amino acid sensor instead (PubMed:25561175, PubMed:25567906). The high concentration of arginine in lysosomes suggests that it acts as an arginine sensor (PubMed:25567906). {ECO:0000269|PubMed:25561175, ECO:0000269|PubMed:25567906}.; ",{"$nulls":4},"p.Gly228Ala","c.683G>C","MODERATE","228/561",6,{"$nulls":5},"5","113","70","98","56","73","59","0","0","0","0.4915",{"$nulls":20},"3.275822","4.42","2.65;.;2.65;.;.;.;.","1","-1.91;-1.51;-1.91;-1.51;-1.58;-1.85;-2.77","1.0;.;1.0;.;.;.;.","0.159;1.0;0.159;0.726;0.136;0.604;1.0","0.705;0.766;0.706;0.712;0.694;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","111,0","0","111","0/1","40,30","0.4286","70",null,"chr5:55664707:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4107"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SMG1","chr16:18829392","SMG1(Y3166S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine protein kinase involved in both mRNA surveillance and genotoxic stress response pathways. Recognizes the substrate consensus sequence [ST]-Q. Plays a central role in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by phosphorylating UPF1/RENT1. Recruited by release factors to stalled ribosomes together with SMG8 and SMG9 (forming the SMG1C protein kinase complex), and UPF1 to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Also acts as a genotoxic stress-activated protein kinase that displays some functional overlap with ATM. Can phosphorylate p53/TP53 and is required for optimal p53/TP53 activation after cellular exposure to genotoxic stress. Its depletion leads to spontaneous DNA damage and increased sensitivity to ionizing radiation (IR). May activate PRKCI but not PRKCZ. {ECO:0000269|PubMed:11331269, ECO:0000269|PubMed:11544179, ECO:0000269|PubMed:15175154, ECO:0000269|PubMed:16452507}.; ",{"$nulls":4},"p.Tyr3166Ser","c.9497A>C","MODERATE","3166/3661",54,{"$nulls":5},"5","802","456","638","333","681","371","0","0","0","0.0809",{"$nulls":20},"3.004163","5.24;5.18","1.905;.","0.755668","-3.84;.","0.003;.","0.096;.","0.808;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their full-length nature has yet to be determined. [provided by RefSeq, Mar 2013].  ",null,null,"0/0","793,0","0","793","0/1","398,29","0.0679","427",null,"chr16:18829392:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0751"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SMG1","chr16:18829392","SMG1(Y3166S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine protein kinase involved in both mRNA surveillance and genotoxic stress response pathways. Recognizes the substrate consensus sequence [ST]-Q. Plays a central role in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by phosphorylating UPF1/RENT1. Recruited by release factors to stalled ribosomes together with SMG8 and SMG9 (forming the SMG1C protein kinase complex), and UPF1 to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Also acts as a genotoxic stress-activated protein kinase that displays some functional overlap with ATM. Can phosphorylate p53/TP53 and is required for optimal p53/TP53 activation after cellular exposure to genotoxic stress. Its depletion leads to spontaneous DNA damage and increased sensitivity to ionizing radiation (IR). May activate PRKCI but not PRKCZ. {ECO:0000269|PubMed:11331269, ECO:0000269|PubMed:11544179, ECO:0000269|PubMed:15175154, ECO:0000269|PubMed:16452507}.; ",{"$nulls":4},"p.Tyr3166Ser","c.9497A>C","MODERATE","3166/3661",54,{"$nulls":5},"5","802","375","638","285","681","303","0","0","0","0.2706",{"$nulls":20},"3.004163","5.24;5.18","1.905;.","0.755668","-3.84;.","0.003;.","0.096;.","0.808;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their full-length nature has yet to be determined. [provided by RefSeq, Mar 2013].  ",null,null,"0/0","804,0","0","804","0/1","266,101","0.2752","367",null,"chr16:18829392:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2877"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SOX17","chr8:54459388","SOX17(P213L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as transcription regulator that binds target promoter DNA and bends the DNA. Binds to the sequences 5'- AACAAT-'3 or 5'-AACAAAG-3'. Modulates transcriptional regulation via WNT3A. Inhibits Wnt signaling. Promotes degradation of activated CTNNB1. Plays a key role in the regulation of embryonic development. Required for normal looping of the embryonic heart tube. Required for normal development of the definitive gut endoderm. Probable transcriptional activator in the premeiotic germ cells (By similarity). {ECO:0000250}.; ","gedi|level2",{"$nulls":3},"p.Pro213Leu","c.638C>T","MODERATE","213/414",2,{"$nulls":5},"4","820","333","586","236","724","284","0","0","0","0.1549",{"$nulls":20},"0.857311","-0.98","1.59","0.999678","-0.89","0.126","0.49","0.097",{"$nulls":3},"Unknown",-1,"AD","Vesicoureteral reflux 3","Renal","kWNT","This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. [provided by RefSeq, Jul 2008].  ",null,"C3150927","0/0","803,0","0","803","0/1","267,51","0.1604","318",null,"chr8:54459388:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1525"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SPEG","chr2:219451142","SPEG(S707L)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs552276513",1.522E-5,"DISEASE: Myopathy, centronuclear, 5 (CNM5) [MIM:615959]: A form of centronuclear myopathy, a congenital muscle disorder characterized by progressive muscular weakness and wasting involving mainly limb girdle, trunk, and neck muscles. It may also affect distal muscles. Weakness may be present during childhood or adolescence or may not become evident until the third decade of life. Ptosis is a frequent clinical feature. The most prominent histopathologic features include high frequency of centrally located nuclei in muscle fibers not secondary to regeneration, radial arrangement of sarcoplasmic strands around the central nuclei, and predominance and hypotrophy of type 1 fibers. CNM5 features include severe neonatal hypotonia with respiratory insufficiency, difficulty feeding, and delayed motor development. Some patients die in infancy, and some develop dilated cardiomyopathy. {ECO:0000269|PubMed:25087613}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 3 may have a role in regulating the growth and differentiation of arterial smooth muscle cells.; ",{"$nulls":4},"p.Ser707Leu","c.2120C>T","MODERATE","707/3267",5,{"$nulls":5},"5","558","213","427","156","423","156","0","0","0","0.2308",{"$nulls":20},"3.87868","-0.25;0.03","0.895;.","0.999991;0.999966;1","-2.87;-3.32","1.0;.","0.002;0.0","0.563;0.768",{"$nulls":3},"ExAC_NFE_AF",1.522E-5,"AR","Centronuclear myopathy 5","Cardiovascular; Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C4014814","0/0","540,0","0","540","0/1","156,40","0.2041","196",null,"chr2:219451142:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1923"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","SPOCK1","chr5:136992552","SPOCK1(W213L)",{"$nulls":6},255,"PASS","Missense","rs1158891066",-1,null,"FUNCTION: May play a role in cell-cell and cell-matrix interactions. May contribute to various neuronal mechanisms in the central nervous system.; ",{"$nulls":4},"p.Trp213Leu","c.638G>T","MODERATE","213/439",7,{"$nulls":5},"4","898","569","603","372","830","517","0","0","0","0.0793",{"$nulls":20},"3.80619","-0.02;.","2.685;.","1","-10.46;.","0.961;.","0.001;.","0.912;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","881,0","0","881","0/1","503,50","0.0904","553",null,"chr5:136992552:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.086"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SPOCK1","chr5:136992552","SPOCK1(W213L)",{"$nulls":6},255,"PASS","Missense","rs1158891066",-1,null,"FUNCTION: May play a role in cell-cell and cell-matrix interactions. May contribute to various neuronal mechanisms in the central nervous system.; ",{"$nulls":4},"p.Trp213Leu","c.638G>T","MODERATE","213/439",7,{"$nulls":5},"4","898","443","603","288","826","422","0","0","0","0.41",{"$nulls":20},"3.80619","-0.02;.","2.685;.","1","-10.46;.","0.961;.","0.001;.","0.912;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","877,0","0","877","0/1","254,175","0.4079","429",null,"chr5:136992552:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4132"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","SPTA1","chr1:158612880","SPTA1(I2357M)",null,null,"domain (EF-hand 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Elliptocytosis 2 (EL2) [MIM:130600]: A Rhesus-unlinked form of hereditary elliptocytosis, a genetically heterogeneous, autosomal dominant hematologic disorder. It is characterized by variable hemolytic anemia and elliptical or oval red cell shape. {ECO:0000269|PubMed:1541680, ECO:0000269|PubMed:1638030, ECO:0000269|PubMed:1679439, ECO:0000269|PubMed:1878597, ECO:0000269|PubMed:2384601, ECO:0000269|PubMed:2568861, ECO:0000269|PubMed:2568862, ECO:0000269|PubMed:2794061, ECO:0000269|PubMed:7772539, ECO:0000269|PubMed:8018926, ECO:0000269|PubMed:8193371, ECO:0000269|PubMed:8364215}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hereditary pyropoikilocytosis (HPP) [MIM:266140]: Autosomal recessive hematologic disorder characterized by hemolytic anemia, microspherocytosis, poikilocytosis, and an unusual thermal sensitivity of red cells. {ECO:0000269|PubMed:1878597}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spherocytosis 3 (SPH3) [MIM:270970]: Spherocytosis is a hematologic disorder leading to chronic hemolytic anemia and characterized by numerous abnormally shaped erythrocytes which are generally spheroidal. SPH3 is characterized by severe hemolytic anemia. Inheritance is autosomal recessive. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Spectrin is the major constituent of the cytoskeletal network underlying the erythrocyte plasma membrane. It associates with band 4.1 and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane.; ","tcga-gbm",{"$nulls":3},"p.Ile2357Met","c.7071A>G","MODERATE","2357/2419",51,{"$nulls":5},"5","834","646","593","435","746","580","0","0","0","0.1328",{"$nulls":20},"2.991028",null,"2.26","0.993675",null,"0.957",null,"0.602;.",{"$nulls":3},"Unknown",-1,"AD/AR","Spherocytosis, type 3; Pyropoikilocytosis , hereditary; Ellipsocytosis 2","Hematologic",{"$nulls":3},"C0520739| C1851741| C2678338","0/0","811,0","0","811","0/1","526,84","0.1377","610",null,"chr1:158612880:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1494"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","STXBP4","chr17:54986248","STXBP4(S10L)",{"$nulls":3},"modified-residue:Phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the translocation of transport vesicles from the cytoplasm to the plasma membrane. Inhibits the translocation of SLC2A4 from intracellular vesicles to the plasma membrane by STX4A binding and preventing the interaction between STX4A and VAMP2. Stimulation with insulin disrupts the interaction with STX4A, leading to increased levels of SLC2A4 at the plasma membrane. May also play a role in the regulation of insulin release by pancreatic beta cells after stimulation by glucose (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ser10Leu","c.29C>T","MODERATE","10/553",3,{"$nulls":5},"5","113","66","74","47","100","58","0","0","0","0.0517",{"$nulls":20},"2.515859","3.75;3.65;3.75","1.845;.;.","0.968016;0.968016;0.968016;1;1","-2.2;-2.03;-2.2","0.181;.;0.651","0.011;0.01;0.012","0.25;0.164;0.197",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","111,0","0","111","0/1","60,4","0.0625","64",null,"chr17:54986248:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0638"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TDRD15","chr2:21139902","TDRD15(S812C)",{"$nulls":6},255,"PASS","Missense","rs955078886",-1,{"$nulls":6},"p.Ser812Cys","c.2435C>G","MODERATE","812/1934",4,{"$nulls":5},"5","909","473","690","369","816","410","0","0","0","0.1439",{"$nulls":20},"3.340411","2.97;.",null,null,"-3.29;.",null,"0.022;.","0.358;0.342",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","894,0","0","894","0/1","388,68","0.1491","456",null,"chr2:21139902:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1491"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","TENM1","chrX:124653753","TENM1(G400A)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. May function as a cellular signal transducer (By similarity). {ECO:0000250}.; FUNCTION: Ten-1 intracellular domain: Induces gene transcription activation. {ECO:0000250}.; ",{"$nulls":4},"p.Gly400Ala","c.1199G>C","MODERATE","400/2732",7,{"$nulls":5},"5","511","290","346","193","483","262","0","0","0","0.0916",{"$nulls":20},"2.884516","1.11","1.65","1","-4.17;-4.1","1.0;.","0.25;0.249","0.676;0.672",{"$nulls":3},"Unknown",-1,"AR","Microphthalmia, isolated, with coloboma 9","Ophthalmologic",null,"The protein encoded by this gene belongs to the tenascin family and teneurin subfamily. It is expressed in the neurons and may function as a cellular signal transducer. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].",null,null,"0/0","504,0","0","504","0/1","248,25","0.0916","273",null,"chrX:124653753:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0933"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TENM1","chrX:124653753","TENM1(G400A)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. May function as a cellular signal transducer (By similarity). {ECO:0000250}.; FUNCTION: Ten-1 intracellular domain: Induces gene transcription activation. {ECO:0000250}.; ",{"$nulls":4},"p.Gly400Ala","c.1199G>C","MODERATE","400/2732",7,{"$nulls":5},"5","511","308","346","209","483","279","0","0","0","0.3477",{"$nulls":20},"2.884516","1.11","1.65","1","-4.17;-4.1","1.0;.","0.25;0.249","0.676;0.672",{"$nulls":3},"Unknown",-1,"AR","Microphthalmia, isolated, with coloboma 9","Ophthalmologic",null,"The protein encoded by this gene belongs to the tenascin family and teneurin subfamily. It is expressed in the neurons and may function as a cellular signal transducer. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].",null,null,"0/0","500,0","0","500","0/1","190,101","0.3471","291",null,"chrX:124653753:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3493"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TENM3","chr4:182673074","TENM3(A394E)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Microphthalmia, isolated, with coloboma, 9 (MCOPCB9) [MIM:615145]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269|PubMed:22766609, ECO:0000269|PubMed:27103084}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in neural development by regulating the establishment of proper connectivity within the nervous system. Acts in both pre- and postsynaptic neurons in the hippocampus to control the assembly of a precise topographic projection: required in both CA1 and subicular neurons for the precise targeting of proximal CA1 axons to distal subiculum, probably by promoting homophilic cell adhesion. Required for proper dendrite morphogenesis and axon targeting in the vertebrate visual system, thereby playing a key role in the development of the visual pathway. Regulates the formation in ipsilateral retinal mapping to both the dorsal lateral geniculate nucleus (dLGN) and the superior colliculus (SC). May also be involved in the differentiation of the fibroblast-like cells in the superficial layer of mandibular condylar cartilage into chondrocytes. {ECO:0000250|UniProtKB:Q9WTS6}.; ",{"$nulls":4},"p.Ala394Glu","c.1181C>A","MODERATE","394/2699",7,{"$nulls":5},"5","377","154","286","115","311","115","0","0","0","0.2609",{"$nulls":20},"2.796646","2.02","2.32","0.998596","-2.56","0.18","0.009","0.611",{"$nulls":3},"Unknown",-1,"AR","Microphthalmia, isolated, with coloboma 9","Ophthalmologic",{"$nulls":3},"C3554592","0/0","368,0","0","368","0/1","113,35","0.2365","148",null,"chr4:182673074:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2087"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TGFBR1","chr9:99105233","TGFBR1(P10S)",null,null,"signal peptide ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Loeys-Dietz syndrome 1 (LDS1) [MIM:609192]: An aortic aneurysm syndrome with widespread systemic involvement, characterized by arterial tortuosity and aneurysms, hypertelorism, and bifid uvula or cleft palate. Physical findings include prominent joint laxity, easy bruising, wide and atrophic scars, velvety and translucent skin with easily visible veins, spontaneous rupture of the spleen or bowel, and catastrophic complications of pregnancy, including rupture of the gravid uterus and the arteries, either during pregnancy or in the immediate postpartum period. Some patients have craniosynostosis, exotropy, micrognathia and retrognathia, structural brain abnormalities, and intellectual deficit. {ECO:0000269|PubMed:15731757, ECO:0000269|PubMed:16596670, ECO:0000269|PubMed:16791849, ECO:0000269|PubMed:16928994, ECO:0000269|PubMed:19883511, ECO:0000269|PubMed:22113417}. Note=The disease is caused by mutations affecting the gene represented in this entry. TGFBR1 mutation Gln-487 has been reported to be associated with thoracic aortic aneurysms and dissection (TAAD) (PubMed:16791849). This phenotype, also known as thoracic aortic aneurysms type 5 (AAT5), is distinguised from LDS1 by having aneurysms restricted to thoracic aorta. It is unclear, however, if this condition is fulfilled in individuals bearing Gln-487 mutation, that is why they are considered as LDS1 by the OMIM resource. {ECO:0000269|PubMed:16791849}.; DISEASE: Multiple self-healing squamous epithelioma (MSSE) [MIM:132800]: A disorder characterized by multiple skin tumors that undergo spontaneous regression. Tumors appear most often on sun-exposed regions, are locally invasive, and undergo spontaneous resolution over a period of months leaving pitted scars. {ECO:0000269|PubMed:21358634}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transmembrane serine/threonine kinase forming with the TGF-beta type II serine/threonine kinase receptor, TGFBR2, the non-promiscuous receptor for the TGF-beta cytokines TGFB1, TGFB2 and TGFB3. Transduces the TGFB1, TGFB2 and TGFB3 signal from the cell surface to the cytoplasm and is thus regulating a plethora of physiological and pathological processes including cell cycle arrest in epithelial and hematopoietic cells, control of mesenchymal cell proliferation and differentiation, wound healing, extracellular matrix production, immunosuppression and carcinogenesis. The formation of the receptor complex composed of 2 TGFBR1 and 2 TGFBR2 molecules symmetrically bound to the cytokine dimer results in the phosphorylation and the activation of TGFBR1 by the constitutively active TGFBR2. Activated TGFBR1 phosphorylates SMAD2 which dissociates from the receptor and interacts with SMAD4. The SMAD2-SMAD4 complex is subsequently translocated to the nucleus where it modulates the transcription of the TGF-beta-regulated genes. This constitutes the canonical SMAD-dependent TGF-beta signaling cascade. Also involved in non- canonical, SMAD-independent TGF-beta signaling pathways. For instance, TGFBR1 induces TRAF6 autoubiquitination which in turn results in MAP3K7 ubiquitination and activation to trigger apoptosis. Also regulates epithelial to mesenchymal transition through a SMAD-independent signaling pathway through PARD6A phosphorylation and activation. {ECO:0000269|PubMed:15761148, ECO:0000269|PubMed:16754747, ECO:0000269|PubMed:18758450, ECO:0000269|PubMed:7774578, ECO:0000269|PubMed:8752209, ECO:0000269|PubMed:8980228, ECO:0000269|PubMed:9346908}.; ","acmg|level2",{"$nulls":3},"p.Pro10Ser","c.28C>T","MODERATE","10/507",1,{"$nulls":5},"4","107","48","64","31",null,null,"0","0",{"$nulls":22},"1.5857839999999999","-1.65;-1.75;-1.72",null,"1","-0.02;0.6;-0.03","0.117;0.0;.","0.689;0.486;0.689","0.093;0.126;0.123",{"$nulls":3},"Unknown",-1,"AD","Loeys-Dietz syndrome, type 1A; Loeys-Dietz syndrome, type 2A","Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Obstetric","kCANCER,kMAPK,kTGF_BETA,vSMAD",null,null,"C4083047| C4707243| C4707243| C4551955","0/0","100,0","0","100","0/1","41,6","0.1277","47",null,"chr9:99105233:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.129"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","TKTL1","chrX:154315338","TKTL1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate. {ECO:0000250}.; ",{"$nulls":5},"c.1029+1G>A","HIGH",null,7,{"$nulls":5},"5","838","509","578","325","779","478","0","0","0","0.1067",{"$nulls":5},"(TKTL1|ENSG00000007350|1|1.00)",{"$nulls":14},"4.88467",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","814,0","0","814","0/1","430,58","0.1189","488",null,"chrX:154315338:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1169"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TKTL1","chrX:154315338","TKTL1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate. {ECO:0000250}.; ",{"$nulls":5},"c.1029+1G>A","HIGH",null,7,{"$nulls":5},"5","838","493","578","336","776","441","0","0","0","0.4376",{"$nulls":5},"(TKTL1|ENSG00000007350|1|1.00)",{"$nulls":14},"4.88467",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","814,0","0","814","0/1","244,220","0.4741","464",null,"chrX:154315338:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4673"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","TM7SF2","chr11:65113575","TM7SF2(R195P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the conversion of lanosterol to cholesterol. {ECO:0000269|PubMed:11784322}.; ",{"$nulls":4},"p.Arg195Pro","c.584G>C","MODERATE","195/418",5,{"$nulls":5},"3",null,null,"325","228","439","311",null,null,"0","0.0611",{"$nulls":20},"4.987182","-5.63","3.965;.;.;.;3.965;.;.;.;.","0.999995;0.999995;0.999998","-5.61;-6.07;-5.5;-5.83;-6.04;-5.5;-6.77;-6.33;-5.9","1.0;.;.;.;1.0;.;.;.;.","0.004;0.001;0.001;0.004;0.003;0.001;0.0;0.001;0.001","0.933;.;.;.;0.939;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","466,1","0.0021","475","0/1","316,19","0.0567","340",null,"chr11:65113575:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.057"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TM7SF2","chr11:65113575","TM7SF2(R195P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the conversion of lanosterol to cholesterol. {ECO:0000269|PubMed:11784322}.; ",{"$nulls":4},"p.Arg195Pro","c.584G>C","MODERATE","195/418",5,{"$nulls":5},"4","475","267","325","179","438","242","0.0021","0.0021","0","0.1322",{"$nulls":20},"4.987182","-5.63","3.965;.;.;.;3.965;.;.;.;.","0.999995;0.999995;0.999998","-5.61;-6.07;-5.5;-5.83;-6.04;-5.5;-6.77;-6.33;-5.9","1.0;.;.;.;1.0;.;.;.;.","0.004;0.001;0.001;0.004;0.003;0.001;0.0;0.001;0.001","0.933;.;.;.;0.939;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","445,0","0","445","0/1","212,40","0.1587","252",null,"chr11:65113575:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1341"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TMEM175","chr4:947773","TMEM175(D12Y)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Parkinson disease (PARK) [MIM:168600]: A complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability. Additional features are characteristic postural abnormalities, dysautonomia, dystonic cramps, and dementia. The pathology of Parkinson disease involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. The disease is progressive and usually manifests after the age of 50 years, although early-onset cases (before 50 years) are known. The majority of the cases are sporadic suggesting a multifactorial etiology based on environmental and genetic factors. However, some patients present with a positive family history for the disease. Familial forms of the disease usually begin at earlier ages and are associated with atypical clinical features. {ECO:0000269|PubMed:28193887}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry. TMEM175 defects result in unstable lysosomal pH, leading to decreased lysosomal catalytic activity, decreased glucocerebrosidase activity, impaired autophagosome clearance by the lysosome and decreased mitochondrial respiration (PubMed:28193887). {ECO:0000269|PubMed:28193887}.; ","FUNCTION: Organelle-specific potassium channel specifically responsible for potassium conductance in endosomes and lysosomes. Forms a potassium-permeable leak-like channel, which regulates lumenal pH stability and is required for autophagosome-lysosome fusion. Constitutes the major lysosomal potassium channel. {ECO:0000269|PubMed:26317472, ECO:0000269|PubMed:28723891}.; ",{"$nulls":4},"p.Asp12Tyr","c.34G>T","MODERATE","12/504",2,{"$nulls":5},"5","671","357","547","282","548","284","0","0","0","0.1831",{"$nulls":20},"1.630963","0.86;1.4;0.82;0.85",".;1.65;.;.","1","-2.57;-3.43;-3.04;-2.65",".;0.948;.;.","0.003;0.002;0.005;0.003",".;0.176;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","653,0","0","653","0/1","286,56","0.1637","342",null,"chr4:947773:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1631"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","TMTC4","chr13:100625893","TMTC4(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.1587-1G>C","HIGH",null,13,{"$nulls":5},"5","224","135","182","113","196","121","0","0","0","0.0661",{"$nulls":5},"(TMTC4|ENSG00000125247|1|1.00)",{"$nulls":14},"5.236443",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","225,0","0","225","0/1","127,9","0.0662","136",null,"chr13:100625893:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0708"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TMTC4","chr13:100625893","TMTC4(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.1587-1G>C","HIGH",null,13,{"$nulls":5},"5","224","112","182","90","196","98","0","0","0","0.2551",{"$nulls":5},"(TMTC4|ENSG00000125247|1|1.00)",{"$nulls":14},"5.236443",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","225,0","0","225","0/1","83,29","0.2589","112",null,"chr13:100625893:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2556"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TOX2","chr20:44051305","TOX2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Putative transcriptional activator involved in the hypothalamo-pituitary-gonadal system.; ",{"$nulls":5},"c.412-1G>C","HIGH",null,3,{"$nulls":5},"5","514","218","416","174","437","169","0","0","0","0.1953",{"$nulls":5},"(TOX2|ENSG00000124191|1|1.00)",{"$nulls":14},"5.68109",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","494,0","0","494","0/1","166,40","0.1942","206",null,"chr20:44051305:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1839"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","TP53","chr17:7675076","TP53(H140L)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In sporadic cancers; somatic mutation. TP53(T140A)), sequence variant (In sporadic cancers; somatic mutation. TP53(T140I)), sequence variant (In a sporadic cancer; somatic mutation; dbSNP:rs786202561. TP53(T140N)), sequence variant (In a sporadic cancer; somatic mutation. TP53(T140P)), sequence variant (In sporadic cancers; somatic mutation. TP53(T140S))",{"$nulls":3},255,"PASS","Missense","rs1057519991",-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.His140Leu","c.419A>T","MODERATE","140/410",5,62,{"$nulls":4},"3","1469","973","1090","680",null,null,"0.0007","0.0007",{"$nulls":22},"2.398992","-7.88;-7.88;.;.;.;.;.;.;.;-7.88;.;.;-7.88;-7.88;.;.;-7.88;.;.;-7.88;-7.88",".;.;.;.;.;.;.;.;.;2.575;.;2.575;2.575;2.575;.;.;2.575;.;.;.;.","1","-10.58;-10.44;.;.;.;.;.;.;.;-10.43;.;.;-10.44;-10.44;.;.;-10.43;.;.;-10.07;-10.49","0.224;.;.;.;.;.;.;.;.;0.333;.;0.679;0.133;0.679;.;.;0.333;.;.;.;1.0","0.007;0.006;.;.;.;.;.;.;.;0.005;.;.;0.005;0.006;.;.;0.005;.;.;0.007;0.022","0.684;0.662;0.59;0.584;0.579;0.567;0.59;0.584;0.668;0.661;0.668;0.66;0.66;0.66;0.68;0.619;0.66;0.668;0.634;.;.",{"$nulls":3},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","1424,0","0","1424","0/1","834,87","0.0945","921",null,"chr17:7675076:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0941"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TP53","chr17:7675076","TP53(H140L)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In sporadic cancers; somatic mutation. TP53(T140A)), sequence variant (In sporadic cancers; somatic mutation. TP53(T140I)), sequence variant (In a sporadic cancer; somatic mutation; dbSNP:rs786202561. TP53(T140N)), sequence variant (In a sporadic cancer; somatic mutation. TP53(T140P)), sequence variant (In sporadic cancers; somatic mutation. TP53(T140S))",{"$nulls":3},255,"PASS","Missense","rs1057519991",-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.His140Leu","c.419A>T","MODERATE","140/410",5,62,{"$nulls":4},"4","1469","699","1090","509","1294","603","0.0007","0.0007","0","0.3383",{"$nulls":20},"2.398992","-7.88;-7.88;.;.;.;.;.;.;.;-7.88;.;.;-7.88;-7.88;.;.;-7.88;.;.;-7.88;-7.88",".;.;.;.;.;.;.;.;.;2.575;.;2.575;2.575;2.575;.;.;2.575;.;.;.;.","1","-10.58;-10.44;.;.;.;.;.;.;.;-10.43;.;.;-10.44;-10.44;.;.;-10.43;.;.;-10.07;-10.49","0.224;.;.;.;.;.;.;.;.;0.333;.;0.679;0.133;0.679;.;.;0.333;.;.;.;1.0","0.007;0.006;.;.;.;.;.;.;.;0.005;.;.;0.005;0.006;.;.;0.005;.;.;0.007;0.022","0.684;0.662;0.59;0.584;0.579;0.567;0.59;0.584;0.668;0.661;0.668;0.66;0.66;0.66;0.68;0.619;0.66;0.668;0.634;.;.",{"$nulls":3},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","1440,0","0","1440","0/1","440,245","0.3577","685",null,"chr17:7675076:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3576"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","TRAPPC2L","chr16:88860110","TRAPPC2L(E171A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:19416478}.; ",{"$nulls":4},"p.Glu171Ala","c.512A>C","MODERATE","171/241",4,{"$nulls":5},"3","1258","839",null,null,"1096","724","0","0","0","0.0511",{"$nulls":20},"-0.160372","-2.73",null,"1","-0.04",null,null,"0.038",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193033","0/0","1235,0","0","1235","0/1","760,41","0.0512","801",null,"chr16:88860110:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TRAPPC2L","chr16:88860110","TRAPPC2L(E171A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:19416478}.; ",{"$nulls":4},"p.Glu171Ala","c.512A>C","MODERATE","171/241",4,{"$nulls":5},"5","1258","706","991","542","1094","614","0","0","0","0.1417",{"$nulls":20},"-0.160372","-2.73",null,"1","-0.04",null,null,"0.038",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193033","0/0","1244,0","0","1244","0/1","587,103","0.1493","690",null,"chr16:88860110:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1605"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TRPM5","chr11:2417826","TRPM5(Q304fs)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Voltage-modulated Ca(2+)-activated, monovalent cation channel (VCAM) that mediates a transient membrane depolarization and plays a central role in taste transduction. Monovalent- specific, non-selective cation channel that mediates the transport of Na(+), K(+) and Cs(+) ions equally well. Activated directly by increases in intracellular Ca(2+), but is impermeable to it. Gating is voltage-dependent and displays rapid activation and deactivation kinetics upon channel stimulation even during sustained elevations in Ca(2+). Also activated by a fast intracellular Ca(2+) increase in response to inositol 1,4,5- triphosphate-producing receptor agonists. The channel is blocked by extracellular acidification. External acidification has 2 effects, a fast reversible block of the current and a slower irreversible enhancement of current inactivation. Is a highly temperature-sensitive, heat activated channel showing a steep increase of inward currents at temperatures between 15 and 35 degrees Celsius. Heat activation is due to a shift of the voltage- dependent activation curve to negative potentials. Activated by arachidonic acid in vitro. May be involved in perception of bitter, sweet and umami tastes. May also be involved in sensing semiochemicals. {ECO:0000269|PubMed:14634208}.; ",{"$nulls":4},"p.Gln304fs","c.909delG","HIGH","303/1173",7,{"$nulls":5},"5","577","235","394","155","489","187","0","0","0","0.1337",{"$nulls":5},"(TRPM5|ENSG00000070985|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","542,0","0","542","0/1","174,36","0.1714","210",null,"chr11:2417826:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1419"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","TTC6","chr14:37795295","TTC6(N1245I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asn1245Ile","c.3734A>T","MODERATE","1245/1886",18,{"$nulls":5},"5","420","352","309","248","342","294","0","0","0","0.2857",{"$nulls":20},"1.389531","0.71",null,null,"-0.98",null,"0.071","0.239",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","405,0","0","405","0/1","252,87","0.2566","339",null,"chr14:37795295:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.254"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ULBP1","chr6:149969358","ULBP1(T208K)",null,null,"region of interest (MHC class I alpha-2 like )",{"$nulls":3},255,"PASS","Missense","rs752844227",1.2770000000000001E-4,null,"FUNCTION: Binds and activates the KLRK1/NKG2D receptor, mediating natural killer cell cytotoxicity. {ECO:0000269|PubMed:11777960}.; ",{"$nulls":4},"p.Thr208Lys","c.623C>A","MODERATE","208/244",3,{"$nulls":5},"4","707","393","500","269","649","356","0","0","0","0.0534",{"$nulls":20},"1.273355","5.57",null,"0.999536","-4.09","0.997","0.002","0.264",{"$nulls":3},"ExAC_SAS_AF",1.2770000000000001E-4,{"$nulls":7},"0/0","703,0","0","703","0/1","363,23","0.0596","386",null,"chr6:149969358:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0632"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ULBP1","chr6:149969358","ULBP1(T208K)",null,null,"region of interest (MHC class I alpha-2 like )",{"$nulls":3},255,"PASS","Missense","rs752844227",1.2770000000000001E-4,null,"FUNCTION: Binds and activates the KLRK1/NKG2D receptor, mediating natural killer cell cytotoxicity. {ECO:0000269|PubMed:11777960}.; ",{"$nulls":4},"p.Thr208Lys","c.623C>A","MODERATE","208/244",3,{"$nulls":5},"4","707","396","500","259","648","352","0","0","0","0.1619",{"$nulls":20},"1.273355","5.57",null,"0.999536","-4.09","0.997","0.002","0.264",{"$nulls":3},"ExAC_SAS_AF",1.2770000000000001E-4,{"$nulls":7},"0/0","704,0","0","704","0/1","326,64","0.1641","390",null,"chr6:149969358:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1776"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","UNC79","chr14:93474297","UNC79(Q118E)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the NALCN sodium channel complex, a cation channel activated either by neuropeptides substance P or neurotensin that controls neuronal excitability. {ECO:0000250}.; ",{"$nulls":4},"p.Gln118Glu","c.352C>G","MODERATE","118/2657",3,{"$nulls":5},"5","1287","657","917","452","1140","580","0","0","0","0.2034",{"$nulls":20},"1.8366449999999999","2.25",".;0;0","0.999997;0.999997;0.999997;1","-0.49",null,"0.256;0.255;0.257","0.257;0.256;0.257",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1248,0","0","1248","0/1","498,124","0.1994","622",null,"chr14:93474297:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1947"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","USH2A","chr1:215674820","USH2A(L4364R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269|PubMed:10729113, ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:11311042, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12525556, ECO:0000269|PubMed:14970843, ECO:0000269|PubMed:15015129, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17405132, ECO:0000269|PubMed:18273898, ECO:0000269|PubMed:18452394, ECO:0000269|PubMed:19683999, ECO:0000269|PubMed:19737284, ECO:0000269|PubMed:20309401, ECO:0000269|PubMed:20440071, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21593743, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22004887, ECO:0000269|PubMed:23737954, ECO:0000269|PubMed:26377068, ECO:0000269|PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in USH2A has been found in a patient with a form of non-syndromic sensorineural hearing loss. {ECO:0000269|PubMed:25388789}.; ","FUNCTION: Involved in hearing and vision.; ",{"$nulls":4},"p.Leu4364Arg","c.13091T>G","MODERATE","4364/5202",63,{"$nulls":5},"4","789","535","628","431","642","439","0","0","0","0.0797",{"$nulls":20},"3.499079","0.3","3.37","0.999991","-3.62","0.971","0.016","0.827",{"$nulls":3},"Unknown",-1,"AR","Usher syndrome, type 2A","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008].",null,"C3151138| C1848634","0/0","783,0","0","783","0/1","488,48","0.0896","536",null,"chr1:215674820:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0812"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","USH2A","chr1:215674820","USH2A(L4364R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269|PubMed:10729113, ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:11311042, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12525556, ECO:0000269|PubMed:14970843, ECO:0000269|PubMed:15015129, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17405132, ECO:0000269|PubMed:18273898, ECO:0000269|PubMed:18452394, ECO:0000269|PubMed:19683999, ECO:0000269|PubMed:19737284, ECO:0000269|PubMed:20309401, ECO:0000269|PubMed:20440071, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21593743, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22004887, ECO:0000269|PubMed:23737954, ECO:0000269|PubMed:26377068, ECO:0000269|PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in USH2A has been found in a patient with a form of non-syndromic sensorineural hearing loss. {ECO:0000269|PubMed:25388789}.; ","FUNCTION: Involved in hearing and vision.; ",{"$nulls":4},"p.Leu4364Arg","c.13091T>G","MODERATE","4364/5202",63,{"$nulls":5},"4","789","599","628","452","642","464","0","0","0","0.2004",{"$nulls":20},"3.499079","0.3","3.37","0.999991","-3.62","0.971","0.016","0.827",{"$nulls":3},"Unknown",-1,"AR","Usher syndrome, type 2A","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008].",null,"C3151138| C1848634","0/0","783,0","0","783","0/1","454,126","0.2172","580",null,"chr1:215674820:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2146"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","VWF","chr12:6011763","VWF(C1899F)",null,null,"disulfide bond , disulfide bond (Or C-1899 with C-1942 ), disulfide bond , splice variant (In isoform 2. )","disulfide-bond:Or_C-1899_with_C-1942","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: von Willebrand disease 1 (VWD1) [MIM:193400]: A common hemorrhagic disorder due to defects in von Willebrand factor protein and resulting in impaired platelet aggregation. Von Willebrand disease type 1 is characterized by partial quantitative deficiency of circulating von Willebrand factor, that is otherwise structurally and functionally normal. Clinical manifestations are mucocutaneous bleeding, such as epistaxis and menorrhagia, and prolonged bleeding after surgery or trauma. {ECO:0000269|PubMed:10887119, ECO:0000269|PubMed:11698279}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: von Willebrand disease 2 (VWD2) [MIM:613554]: A hemorrhagic disorder due to defects in von Willebrand factor protein and resulting in altered platelet aggregation. Von Willebrand disease type 2 is characterized by qualitative deficiency and functional anomalies of von Willebrand factor. It is divided in different subtypes including 2A, 2B, 2M and 2N (Normandy variant). The mutant VWF protein in types 2A, 2B and 2M are defective in their platelet-dependent function, whereas the mutant protein in type 2N is defective in its ability to bind factor VIII. Clinical manifestations are mucocutaneous bleeding, such as epistaxis and menorrhagia, and prolonged bleeding after surgery or trauma. {ECO:0000269|PubMed:12406074, ECO:0000269|PubMed:1409710, ECO:0000269|PubMed:1419803, ECO:0000269|PubMed:1419804, ECO:0000269|PubMed:1420817, ECO:0000269|PubMed:1429668, ECO:0000269|PubMed:1672694, ECO:0000269|PubMed:1673047, ECO:0000269|PubMed:1729889, ECO:0000269|PubMed:1761120, ECO:0000269|PubMed:1832934, ECO:0000269|PubMed:1906179, ECO:0000269|PubMed:2010538, ECO:0000269|PubMed:2011604, ECO:0000269|PubMed:21592258, ECO:0000269|PubMed:2786201, ECO:0000269|PubMed:7620154, ECO:0000269|PubMed:7734373, ECO:0000269|PubMed:7789955, ECO:0000269|PubMed:8011991, ECO:0000269|PubMed:8123843, ECO:0000269|PubMed:8123844, ECO:0000269|PubMed:8338947, ECO:0000269|PubMed:8348943, ECO:0000269|PubMed:8376405, ECO:0000269|PubMed:8435341, ECO:0000269|PubMed:8486782, ECO:0000269|PubMed:8547152, ECO:0000269|PubMed:8622978}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: von Willebrand disease 3 (VWD3) [MIM:277480]: A severe hemorrhagic disorder due to a total or near total absence of von Willebrand factor in the plasma and cellular compartments, also leading to a profound deficiency of plasmatic factor VIII. Bleeding usually starts in infancy and can include epistaxis, recurrent mucocutaneous bleeding, excessive bleeding after minor trauma, and hemarthroses. {ECO:0000269|PubMed:10887119, ECO:0000269|PubMed:7989040, ECO:0000269|PubMed:8088787}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Important in the maintenance of hemostasis, it promotes adhesion of platelets to the sites of vascular injury by forming a molecular bridge between sub-endothelial collagen matrix and platelet-surface receptor complex GPIb-IX-V. Also acts as a chaperone for coagulation factor VIII, delivering it to the site of injury, stabilizing its heterodimeric structure and protecting it from premature clearance from plasma.; ",{"$nulls":4},"p.Cys1899Phe","c.5696G>T","MODERATE","1899/2813",34,{"$nulls":5},"4",null,null,"247","221","415","101",null,null,"0","0.1089",{"$nulls":20},"4.00483","0.14","2.545","1","-5.45","0.999",null,"0.978",{"$nulls":3},"Unknown",-1,"AD","von Willebrand disease, type 1; von Willebrand disease, type 2A; von Willebrand disease, type 3","Hematologic",{"$nulls":3},"C1848525| C1264039| C1264040","0/0","348,0","0","348","0/1","275,18","0.0614","293",null,"chr12:6011763:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0588"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","VWF","chr12:6011763","VWF(C1899F)",null,null,"disulfide bond , disulfide bond (Or C-1899 with C-1942 ), disulfide bond , splice variant (In isoform 2. )","disulfide-bond:Or_C-1899_with_C-1942","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: von Willebrand disease 1 (VWD1) [MIM:193400]: A common hemorrhagic disorder due to defects in von Willebrand factor protein and resulting in impaired platelet aggregation. Von Willebrand disease type 1 is characterized by partial quantitative deficiency of circulating von Willebrand factor, that is otherwise structurally and functionally normal. Clinical manifestations are mucocutaneous bleeding, such as epistaxis and menorrhagia, and prolonged bleeding after surgery or trauma. {ECO:0000269|PubMed:10887119, ECO:0000269|PubMed:11698279}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: von Willebrand disease 2 (VWD2) [MIM:613554]: A hemorrhagic disorder due to defects in von Willebrand factor protein and resulting in altered platelet aggregation. Von Willebrand disease type 2 is characterized by qualitative deficiency and functional anomalies of von Willebrand factor. It is divided in different subtypes including 2A, 2B, 2M and 2N (Normandy variant). The mutant VWF protein in types 2A, 2B and 2M are defective in their platelet-dependent function, whereas the mutant protein in type 2N is defective in its ability to bind factor VIII. Clinical manifestations are mucocutaneous bleeding, such as epistaxis and menorrhagia, and prolonged bleeding after surgery or trauma. {ECO:0000269|PubMed:12406074, ECO:0000269|PubMed:1409710, ECO:0000269|PubMed:1419803, ECO:0000269|PubMed:1419804, ECO:0000269|PubMed:1420817, ECO:0000269|PubMed:1429668, ECO:0000269|PubMed:1672694, ECO:0000269|PubMed:1673047, ECO:0000269|PubMed:1729889, ECO:0000269|PubMed:1761120, ECO:0000269|PubMed:1832934, ECO:0000269|PubMed:1906179, ECO:0000269|PubMed:2010538, ECO:0000269|PubMed:2011604, ECO:0000269|PubMed:21592258, ECO:0000269|PubMed:2786201, ECO:0000269|PubMed:7620154, ECO:0000269|PubMed:7734373, ECO:0000269|PubMed:7789955, ECO:0000269|PubMed:8011991, ECO:0000269|PubMed:8123843, ECO:0000269|PubMed:8123844, ECO:0000269|PubMed:8338947, ECO:0000269|PubMed:8348943, ECO:0000269|PubMed:8376405, ECO:0000269|PubMed:8435341, ECO:0000269|PubMed:8486782, ECO:0000269|PubMed:8547152, ECO:0000269|PubMed:8622978}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: von Willebrand disease 3 (VWD3) [MIM:277480]: A severe hemorrhagic disorder due to a total or near total absence of von Willebrand factor in the plasma and cellular compartments, also leading to a profound deficiency of plasmatic factor VIII. Bleeding usually starts in infancy and can include epistaxis, recurrent mucocutaneous bleeding, excessive bleeding after minor trauma, and hemarthroses. {ECO:0000269|PubMed:10887119, ECO:0000269|PubMed:7989040, ECO:0000269|PubMed:8088787}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Important in the maintenance of hemostasis, it promotes adhesion of platelets to the sites of vascular injury by forming a molecular bridge between sub-endothelial collagen matrix and platelet-surface receptor complex GPIb-IX-V. Also acts as a chaperone for coagulation factor VIII, delivering it to the site of injury, stabilizing its heterodimeric structure and protecting it from premature clearance from plasma.; ",{"$nulls":4},"p.Cys1899Phe","c.5696G>T","MODERATE","1899/2813",34,{"$nulls":5},"3",null,null,"247","319",{"$nulls":26},"4.00483","0.14","2.545","1","-5.45","0.999",null,"0.978",{"$nulls":3},"Unknown",-1,"AD","von Willebrand disease, type 1; von Willebrand disease, type 2A; von Willebrand disease, type 3","Hematologic",{"$nulls":3},"C1848525| C1264039| C1264040","0/0","345,0","0","345","0/1","393,34","0.0796","427",null,"chr12:6011763:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0627"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","WDR4","chr21:42855747","WDR4(G221S)",{"$nulls":6},255,"PASS","Missense","rs369193067",0.0001475,null,"FUNCTION: Required for the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. In the complex, it is required to stabilize and induce conformational changes of the catalytic subunit. {ECO:0000255|HAMAP-Rule:MF_03056, ECO:0000269|PubMed:12403464}.; ",{"$nulls":4},"p.Gly221Ser","c.661G>A","MODERATE","221/412",7,{"$nulls":5},"5","376","337","287","235","320","295","0","0","0","0.1017",{"$nulls":20},"3.408238","1.25","2.57","0.999993","-5.83","1.0","0.0","0.881;0.88",{"$nulls":3},"ExAC_NFE_AF",0.0001475,{"$nulls":6},"C5193043| C5193042","0/0","369,0","0","369","0/1","285,37","0.1149","322",null,"chr21:42855747:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1106"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","WDR87","chr19:37889738","WDR87(F1311L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe1311Leu","c.3933T>G","MODERATE","1311/2912",6,{"$nulls":5},"5","1247","752","977","550","1083","629","0","0","0","0.0986",{"$nulls":20},"-0.433253","3.26",null,"1","1.0","0.0;.","1.0","0.059;0.029",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1226,0","0","1226","0/1","659,74","0.101","733",null,"chr19:37889738:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0964"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","WDR87","chr19:37889738","WDR87(F1311L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe1311Leu","c.3933T>G","MODERATE","1311/2912",6,{"$nulls":5},"5","1247","662","977","496","1080","565","0","0","0","0.3186",{"$nulls":20},"-0.433253","3.26",null,"1","1.0","0.0;.","1.0","0.059;0.029",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1219,0","0","1219","0/1","439,204","0.3173","643",null,"chr19:37889738:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3206"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZC3H12D","chr6:149451260","ZC3H12D(S336Y)",null,null,"region of interest (Necessary for interaction with ZC3H12A ), splice variant (In isoform 2. ), splice variant (In isoform 3. )","modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving ZC3H12D may be the cause of the transformation of follicular lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL). Translocation t(2;6)(p12;q25) with IGK. Resulting protein may not be expressed.; ","FUNCTION: May regulate cell growth likely by suppressing RB1 phosphorylation (PubMed:19531561). May function as RNase and regulate the levels of target RNA species (Potential). In association with ZC3H12A enhances the degradation of interleukin IL-6 mRNA level in activated macrophages (PubMed:26134560). Serve as a tumor suppressor in certain leukemia cells (PubMed:17210687). Overexpression inhibits the G1 to S phase progression through suppression of RB1 phosphorylation (PubMed:19531561). {ECO:0000269|PubMed:17210687, ECO:0000269|PubMed:19531561, ECO:0000269|PubMed:26134560, ECO:0000305}.; ",{"$nulls":4},"p.Ser336Tyr","c.1007C>A","MODERATE","336/527",6,{"$nulls":5},"5","110","37","89","28","94","30","0","0","0","0.1667",{"$nulls":20},"1.1818089999999999","1.41","0.345","0.996604;0.996604;1;1","-1.64","0.875","0.031","0.083",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","108,0","0","108","0/1","28,8","0.2222","36",null,"chr6:149451260:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2143"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ZCCHC3","chr20:298620","ZCCHC3(G346fs)",null,null,"zinc finger region (CCHC-type 1 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gly346fs","c.1037_1047delGCAGCTGCACG","HIGH","346/403",1,{"$nulls":5},"4",null,null,"516","295","548","314",null,null,"0","0.0701",{"$nulls":5},"(ZCCHC3|ENSG00000247315|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","680,0","0","680","0/1","351,24","0.064","375",null,"chr20:298620:GCGGCAGCTGCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.078"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZCCHC3","chr20:298620","ZCCHC3(G346fs)",null,null,"zinc finger region (CCHC-type 1 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gly346fs","c.1037_1047delGCAGCTGCACG","HIGH","346/403",1,{"$nulls":5},"5","635","248","516","196","548","217","0","0","0","0.4101",{"$nulls":5},"(ZCCHC3|ENSG00000247315|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","680,0","0","680","0/1","138,102","0.425","240",null,"chr20:298620:GCGGCAGCTGCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3469"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZFP2","chr5:178931603","ZFP2(V97G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable transcription factor involved in neuronal differentiation and/or phenotypic maintenance. {ECO:0000250}.; ",{"$nulls":4},"p.Val97Gly","c.290T>G","MODERATE","97/461",5,{"$nulls":5},"5","414","194","345","149","332","153","0","0","0","0.1503",{"$nulls":20},"2.597978","3.17","0.635","0.999995","-2.6","0.025","0.001","0.173;0.27;0.269",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","414,0","0","414","0/1","160,30","0.1579","190",null,"chr5:178931603:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1611"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ZNF160","chr19:53068613","ZNF160(R641G)",null,null,"zinc finger region (C2H2-type 14 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Arg641Gly","c.1921C>G","MODERATE","641/818",6,{"$nulls":5},"4","1098","605","841","451","667","382","0","0","0","0.0628",{"$nulls":20},"1.782731","1.84","2.26;2.26;2.26;.","1",".;-4.49;-4.49;.","0.829;0.829;0.829;.",".;0.003;0.003;.","0.183;0.188;0.171;0.17",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1059,0","0","1059","0/1","519,34","0.0615","553",null,"chr19:53068613:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0621"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF160","chr19:53068613","ZNF160(R641G)",null,null,"zinc finger region (C2H2-type 14 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Arg641Gly","c.1921C>G","MODERATE","641/818",6,{"$nulls":5},"4","1098","452","841","343","665","262","0","0","0","0.2939",{"$nulls":20},"1.782731","1.84","2.26;2.26;2.26;.","1",".;-4.49;-4.49;.","0.829;0.829;0.829;.",".;0.003;0.003;.","0.183;0.188;0.171;0.17",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1060,0","0","1060","0/1","300,135","0.3103","435",null,"chr19:53068613:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.312"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF208","chr19:21974623","ZNF208(L137F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Leu137Phe","c.411G>C","MODERATE","137/1280",4,{"$nulls":5},"5","190","113","153","92","167","96","0","0","0","0.3229",{"$nulls":20},"-0.352699",".;3.11",".;2.425","1",".;-1.26",".;0.125",".;0.308","0.052;0.037",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","190,0","0","190","0/1","73,39","0.3482","112",null,"chr19:21974623:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.3478"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF334","chr20:46502065","ZNF334(R448I)",{"$nulls":6},255,"PASS","Missense","rs1337852854",-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Arg448Ile","c.1343G>T","MODERATE","448/703",4,1,{"$nulls":4},"4","693","426","572","341","530","343","0","0","0","0.1574",{"$nulls":20},"2.613126",".;1.83;1.83;1.83;.",".;2.22;.;.;.","0.999825",".;-6.32;-6.37;.;.",".;0.999;.;0.999;.",".;0.118;0.123;.;.","0.279;0.277;0.362;0.423;0.321",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","691,0","0","691","0/1","352,71","0.1678","423",null,"chr20:46502065:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1642"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ZNF48","chr16:30398961","ZNF48(Y571D)",null,null,"zinc finger region (C2H2-type 12 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Tyr571Asp","c.1711T>G","MODERATE","571/618",2,{"$nulls":5},"4","1483","987","1166","742","1242","815","0","0","0","0.1006",{"$nulls":20},"4.05771",".;.;1.79",".;3.67;3.67","0.995249",".;.;-7.92",".;1.0;1.0",".;.;0.002","0.666;0.712;0.713",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1429,0","0","1429","0/1","852,93","0.0984","945",null,"chr16:30398961:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.097"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF48","chr16:30398961","ZNF48(Y571D)",null,null,"zinc finger region (C2H2-type 12 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Tyr571Asp","c.1711T>G","MODERATE","571/618",2,{"$nulls":5},"5","1483","787","1166","611","1243","682","0","0","0","0.2434",{"$nulls":20},"4.05771",".;.;1.79",".;3.67;3.67","0.995249",".;.;-7.92",".;1.0;1.0",".;.;0.002","0.666;0.712;0.713",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1427,0","0","1427","0/1","577,178","0.2358","755",null,"chr16:30398961:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2406"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ZNF551","chr19:57686820","ZNF551(T182S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Thr182Ser","c.545C>G","MODERATE","182/670",3,{"$nulls":5},"5","709","426","538","299","657","382","0","0","0","0.0916",{"$nulls":20},"-0.376027","3.25;3.4",".;0.76","1",null,".;0.175",null,".;0.046",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","711,0","0","711","0/1","373,37","0.0902","410",null,"chr19:57686820:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0836"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF551","chr19:57686820","ZNF551(T182S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Thr182Ser","c.545C>G","MODERATE","182/670",3,{"$nulls":5},"5","709","326","538","228","655","273","0","0","0","0.3993",{"$nulls":20},"-0.376027","3.25;3.4",".;0.76","1",null,".;0.175",null,".;0.046",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","715,0","0","715","0/1","188,133","0.4143","321",null,"chr19:57686820:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3991"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF644","chr1:90937501","ZNF644(D1224E)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1338002833",-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp1224Glu","c.3672C>G","MODERATE","1224/1327",4,{"$nulls":5},"4","311","220",null,null,"239","157","0","0","0","0.1338",{"$nulls":20},"2.119986","6.38","0.975","0.792168;0.792168;1;1","-0.37","0.924","0.025","0.58;0.541",{"$nulls":3},"Unknown",-1,"AD","Myopia 21, autosomal dominant","Ophthalmologic",{"$nulls":3},"C3279997","0/0","314,0","0","314","0/1","190,25","0.1163","215",null,"chr1:90937501:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZNF841","chr19:52065448","ZNF841(Q812E)",{"$nulls":6},255,"PASS","Missense","rs755610830",2.0810000000000002E-4,null,"FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.; ",{"$nulls":4},"p.Gln812Glu","c.2434C>G","MODERATE","812/924",4,{"$nulls":5},"5","828","323","648","255","487","199","0","0","0","0.1809",{"$nulls":20},"0.813756","3.2",".;.;0.645","1","-1.62;.;-1.7","0.986;0.986;0.947","0.011;.;0.029","0.169;0.169;0.135",{"$nulls":3},"ExAC_AFR_AF",2.0810000000000002E-4,{"$nulls":7},"0/0","812,0","0","812","0/1","266,47","0.1502","313",null,"chr19:52065448:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1569"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ZPBP2","chr17:39872490","ZPBP2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Is implicated in sperm-oocyte interaction during fertilization. {ECO:0000250|UniProtKB:Q6X786}.; ",{"$nulls":5},"c.625+2T>A","HIGH",null,5,{"$nulls":5},"4","81","49","66","46",null,null,"0","0",{"$nulls":7},"(ZPBP2|ENSG00000186075|1|1.00)",{"$nulls":14},"5.466801",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","81,0","0","81","0/1","43,8","0.1569","51",null,"chr17:39872490:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1739"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZPBP2","chr17:39872490","ZPBP2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Is implicated in sperm-oocyte interaction during fertilization. {ECO:0000250|UniProtKB:Q6X786}.; ",{"$nulls":5},"c.625+2T>A","HIGH",null,5,{"$nulls":5},"3","81","45","66","34",null,null,"0","0",{"$nulls":7},"(ZPBP2|ENSG00000186075|1|1.00)",{"$nulls":14},"5.466801",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","81,0","0","81","0/1","24,21","0.4667","45",null,"chr17:39872490:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4706"]
["06BH","T11","JLPIKTOR_JLPIKTOR_17113006BH","ZXDA","chrX:57910245","ZXDA(R59H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes. {ECO:0000269|PubMed:17493635}.; ",{"$nulls":4},"p.Arg59His","c.176G>A","MODERATE","59/799",1,{"$nulls":5},"4",null,null,"406","212","538","228",null,null,"0","0.057",{"$nulls":20},"0.902693","2.79","1.935","1","-0.62","0.955","0.249","0.079",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","557,0","0","557","0/1","280,19","0.0635","299",null,"chrX:57910245:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.066"]
["06BH","T12","JLPIKTOR_JLPIKTOR_17113006BH","ZXDA","chrX:57910245","ZXDA(R59H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes. {ECO:0000269|PubMed:17493635}.; ",{"$nulls":4},"p.Arg59His","c.176G>A","MODERATE","59/799",1,{"$nulls":5},"5","561","202","406","134","534","147","0","0","0","0.2585",{"$nulls":20},"0.902693","2.79","1.935","1","-0.62","0.955","0.249","0.079",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","552,0","0","552","0/1","148,48","0.2449","196",null,"chrX:57910245:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113006BH","somatic","somatic","JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113006BH/somatic/JLPIKTOR_17113006BH_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113006BH_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2239"]

{"sheet":"08DJ","index":5,"n_rows":140,"n_cols":107,"rows_kept":140}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ABCD1","chrX:153726095","ABCD1(G277R)",null,null,"domain (ABC transmembrane type-1 ), sequence variant (In ALD; ADO-type. ABCD1(G277GN)), sequence variant (In ALD; AMN-type. ABCD1(G277R)), sequence variant (In ALD. ABCD1(G277W))",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Adrenoleukodystrophy (ALD) [MIM:300100]: A peroxisomal metabolic disorder characterized by progressive multifocal demyelination of the central nervous system and by peripheral adrenal insufficiency (Addison disease). It results in mental deterioration, corticospinal tract dysfunction, and cortical blindness. Different clinical manifestations exist like: cerebral childhood ALD (CALD), adult cerebral ALD (ACALD), adrenomyeloneuropathy (AMN) and 'Addison disease only' (ADO) phenotype. {ECO:0000269|PubMed:10369742, ECO:0000269|PubMed:10480364, ECO:0000269|PubMed:10551832, ECO:0000269|PubMed:10737980, ECO:0000269|PubMed:10980539, ECO:0000269|PubMed:11248239, ECO:0000269|PubMed:11438993, ECO:0000269|PubMed:11810273, ECO:0000269|PubMed:15643618, ECO:0000269|PubMed:21700483, ECO:0000269|PubMed:21889498, ECO:0000269|PubMed:23651979, ECO:0000269|PubMed:26686776, ECO:0000269|PubMed:7581394, ECO:0000269|PubMed:7717396, ECO:0000269|PubMed:7825602, ECO:0000269|PubMed:7849723, ECO:0000269|PubMed:7904210, ECO:0000269|PubMed:8040304, ECO:0000269|PubMed:8566952, ECO:0000269|PubMed:8651290, ECO:0000269|PubMed:9452087}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=The promoter region of ABCD1 is deleted in the chromosome Xq28 deletion syndrome which involves ABCD1 and the neighboring gene BCAP31. {ECO:0000269|PubMed:11992258}.; ","FUNCTION: Plays a role in the transport of free very-long-chain fatty acids (VLCFAs) as well as their CoA-esters across the peroxisomal membrane by acting as an ATP-specific binding subunit releasing ADP after ATP hydrolysis (PubMed:15682271, PubMed:11248239, PubMed:16946495). Thus, plays a role in regulation of VLCFAs and energy metabolism namely, in the degradation and biosynthesis of fatty acids by beta-oxidation, mitochondrial function and microsomal fatty acid elongation (PubMed:23671276). Involved in several processes; namely, controls the active myelination phase by negatively regulating the microsomal fatty acid elongation activity and may also play a role in axon and myelin maintenance. Controls also the cellular response to oxidative stress by regulating mitochondrial function like, mitochondrial oxidative phosphorylation and depolarization. And finally controls the inflammatory response by positively regulating peroxisomal beta-oxidation of VLCFAs (By similarity). {ECO:0000250|UniProtKB:P48410, ECO:0000269|PubMed:11248239, ECO:0000269|PubMed:15682271, ECO:0000269|PubMed:16946495, ECO:0000269|PubMed:23671276}.; ","mitocarta",{"$nulls":3},"p.Gly277Arg","c.829G>A","MODERATE","277/745",1,{"$nulls":5},"5","551","400","432","293","471","354","0","0","0","0.065",{"$nulls":20},"4.233827","-7.16","3.6;.","1","-7.33;-7.76","1.0;.","0.0","0.869;0.998",{"$nulls":3},"Unknown",-1,"XL","Adrenoleukodystrophy","Biochemical; Endocrine; Neurologic",{"$nulls":3},"C0162309","0/0","548,0","0","548","0/1","372,25","0.063","397",null,"chrX:153726095:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0648"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ACTB","chr7:5528084","ACTB(G302S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Dystonia, juvenile-onset (DJO) [MIM:607371]: A form of dystonia with juvenile onset. Dystonia is defined by the presence of sustained involuntary muscle contraction, often leading to abnormal postures. Patients with juvenile-onset dystonia manifest progressive, generalized, dopa-unresponsive dystonia, developmental malformations and sensory hearing loss. {ECO:0000269|PubMed:16685646}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Baraitser-Winter syndrome 1 (BRWS1) [MIM:243310]: A rare developmental disorder characterized by the combination of congenital ptosis, high-arched eyebrows, hypertelorism, ocular colobomata, and a brain malformation consisting of anterior- predominant lissencephaly. Other typical features include postnatal short stature and microcephaly, intellectual disability, seizures, and hearing loss. {ECO:0000269|PubMed:22366783}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Actin is a highly conserved protein that polymerizes to produce filaments that form cross-linked networks in the cytoplasm of cells (PubMed:29581253). Actin exists in both monomeric (G- actin) and polymeric (F-actin) forms, both forms playing key functions, such as cell motility and contraction (PubMed:29581253). In addition to their role in the cytoplasmic cytoskeleton, G- and F-actin also localize in the nucleus, and regulate gene transcription and motility and repair of damaged DNA (PubMed:29925947). {ECO:0000269|PubMed:29581253, ECO:0000269|PubMed:29925947}.; ",{"$nulls":4},"p.Gly302Ser","c.904G>A","MODERATE","302/375",5,{"$nulls":5},"4","742","670","628","566","660","598","0","0","0","0.1806",{"$nulls":20},"3.921345","-6.0;.;.;.","3.83;3.83;3.83;.","0.999999","-4.16;.;.;.","0.269;0.269;0.269;.",null,"0.989;.;.;.",{"$nulls":3},"Unknown",-1,"AD","Dystonia, juvenile-onset; Baraitser-Winter syndrome 2","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic ",null,"This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, and integrity. This actin is a major constituent of the contractile apparatus and one of the two nonmuscle cytoskeletal actins. [provided by RefSeq, Jul 2008].  ",null,"C1846331| C1855722","0/0","738,0","0","738","0/1","540,128","0.1916","668",null,"chr7:5528084:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1926"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ACTB","chr7:5528084","ACTB(G302S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Dystonia, juvenile-onset (DJO) [MIM:607371]: A form of dystonia with juvenile onset. Dystonia is defined by the presence of sustained involuntary muscle contraction, often leading to abnormal postures. Patients with juvenile-onset dystonia manifest progressive, generalized, dopa-unresponsive dystonia, developmental malformations and sensory hearing loss. {ECO:0000269|PubMed:16685646}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Baraitser-Winter syndrome 1 (BRWS1) [MIM:243310]: A rare developmental disorder characterized by the combination of congenital ptosis, high-arched eyebrows, hypertelorism, ocular colobomata, and a brain malformation consisting of anterior- predominant lissencephaly. Other typical features include postnatal short stature and microcephaly, intellectual disability, seizures, and hearing loss. {ECO:0000269|PubMed:22366783}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Actin is a highly conserved protein that polymerizes to produce filaments that form cross-linked networks in the cytoplasm of cells (PubMed:29581253). Actin exists in both monomeric (G- actin) and polymeric (F-actin) forms, both forms playing key functions, such as cell motility and contraction (PubMed:29581253). In addition to their role in the cytoplasmic cytoskeleton, G- and F-actin also localize in the nucleus, and regulate gene transcription and motility and repair of damaged DNA (PubMed:29925947). {ECO:0000269|PubMed:29581253, ECO:0000269|PubMed:29925947}.; ",{"$nulls":4},"p.Gly302Ser","c.904G>A","MODERATE","302/375",5,{"$nulls":5},"5","742","553","628","444","660","484","0","0","0","0.219",{"$nulls":20},"3.921345","-6.0;.;.;.","3.83;3.83;3.83;.","0.999999","-4.16;.;.;.","0.269;0.269;0.269;.",null,"0.989;.;.;.",{"$nulls":3},"Unknown",-1,"AD","Dystonia, juvenile-onset; Baraitser-Winter syndrome 2","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic ",null,"This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, and integrity. This actin is a major constituent of the contractile apparatus and one of the two nonmuscle cytoskeletal actins. [provided by RefSeq, Jul 2008].  ",null,"C1846331| C1855722","0/0","746,0","0","746","0/1","432,119","0.216","551",null,"chr7:5528084:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2207"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ADAR","chr1:154608000","ADAR(P3A)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense","rs1313399962",-1,"DISEASE: Dyschromatosis symmetrica hereditaria (DSH) [MIM:127400]: An autosomal dominant pigmentary genodermatosis characterized by a mixture of hyperpigmented and hypopigmented macules distributed on the face and the dorsal parts of the hands and feet, that appear in infancy or early childhood. {ECO:0000269|PubMed:12916015, ECO:0000269|PubMed:15146470, ECO:0000269|PubMed:15659327}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Aicardi-Goutieres syndrome 6 (AGS6) [MIM:615010]: A form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood. {ECO:0000269|PubMed:23001123}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) referred to as A-to-I RNA editing (PubMed:7972084, PubMed:7565688, PubMed:12618436). This may affect gene expression and function in a number of ways that include mRNA translation by changing codons and hence the amino acid sequence of proteins; pre-mRNA splicing by altering splice site recognition sequences; RNA stability by changing sequences involved in nuclease recognition; genetic stability in the case of RNA virus genomes by changing sequences during viral RNA replication; and RNA structure-dependent activities such as microRNA production or targeting or protein-RNA interactions. Can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing). Its cellular RNA substrates include: bladder cancer- associated protein (BLCAP), neurotransmitter receptors for glutamate (GRIA2) and serotonin (HTR2C) and GABA receptor (GABRA3). Site-specific RNA editing of transcripts encoding these proteins results in amino acid substitutions which consequently alters their functional activities. Exhibits low-level editing at the GRIA2 Q/R site, but edits efficiently at the R/G site and HOTSPOT1. Its viral RNA substrates include: hepatitis C virus (HCV), vesicular stomatitis virus (VSV), measles virus (MV), hepatitis delta virus (HDV), and human immunodeficiency virus type 1 (HIV-1). Exhibits either a proviral (HDV, MV, VSV and HIV-1) or an antiviral effect (HCV) and this can be editing-dependent (HDV and HCV), editing-independent (VSV and MV) or both (HIV-1). Impairs HCV replication via RNA editing at multiple sites. Enhances the replication of MV, VSV and HIV-1 through an editing- independent mechanism via suppression of EIF2AK2/PKR activation and function. Stimulates both the release and infectivity of HIV-1 viral particles by an editing-dependent mechanism where it associates with viral RNAs and edits adenosines in the 5'UTR and the Rev and Tat coding sequence. Can enhance viral replication of HDV via A-to-I editing at a site designated as amber/W, thereby changing an UAG amber stop codon to an UIG tryptophan (W) codon that permits synthesis of the large delta antigen (L-HDAg) which has a key role in the assembly of viral particles. However, high levels of ADAR1 inhibit HDV replication. {ECO:0000269|PubMed:12618436, ECO:0000269|PubMed:15556947, ECO:0000269|PubMed:15858013, ECO:0000269|PubMed:16120648, ECO:0000269|PubMed:16475990, ECO:0000269|PubMed:17079286, ECO:0000269|PubMed:19605474, ECO:0000269|PubMed:19651874, ECO:0000269|PubMed:19710021, ECO:0000269|PubMed:19908260, ECO:0000269|PubMed:21289159, ECO:0000269|PubMed:22278222, ECO:0000269|PubMed:7565688, ECO:0000269|PubMed:7972084}.; ",{"$nulls":4},"p.Pro3Ala","c.7C>G","MODERATE","3/1226",1,{"$nulls":5},"5","917","1025","640","692","816","916","0","0","0","0.0502",{"$nulls":20},"2.7271330000000003","2.79;.;.","0.69","1;1;0.997788","-0.9;.;.","0.734;0.734;0.827","0.031;.;.","0.315;.;.",{"$nulls":3},"Unknown",-1,"AD/AR","Dyschromatosis symmetrica hereditaria; Aicardi-Goutieres syndrome 6","Dermatologic; Hematologic; Neurologic",{"$nulls":3},"C3539013| C0406775","0/0","892,0","0","892","0/1","924,69","0.0695","993",null,"chr1:154608000:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0578"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ADAR","chr1:154608000","ADAR(P3A)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense","rs1313399962",-1,"DISEASE: Dyschromatosis symmetrica hereditaria (DSH) [MIM:127400]: An autosomal dominant pigmentary genodermatosis characterized by a mixture of hyperpigmented and hypopigmented macules distributed on the face and the dorsal parts of the hands and feet, that appear in infancy or early childhood. {ECO:0000269|PubMed:12916015, ECO:0000269|PubMed:15146470, ECO:0000269|PubMed:15659327}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Aicardi-Goutieres syndrome 6 (AGS6) [MIM:615010]: A form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood. {ECO:0000269|PubMed:23001123}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA) referred to as A-to-I RNA editing (PubMed:7972084, PubMed:7565688, PubMed:12618436). This may affect gene expression and function in a number of ways that include mRNA translation by changing codons and hence the amino acid sequence of proteins; pre-mRNA splicing by altering splice site recognition sequences; RNA stability by changing sequences involved in nuclease recognition; genetic stability in the case of RNA virus genomes by changing sequences during viral RNA replication; and RNA structure-dependent activities such as microRNA production or targeting or protein-RNA interactions. Can edit both viral and cellular RNAs and can edit RNAs at multiple sites (hyper-editing) or at specific sites (site-specific editing). Its cellular RNA substrates include: bladder cancer- associated protein (BLCAP), neurotransmitter receptors for glutamate (GRIA2) and serotonin (HTR2C) and GABA receptor (GABRA3). Site-specific RNA editing of transcripts encoding these proteins results in amino acid substitutions which consequently alters their functional activities. Exhibits low-level editing at the GRIA2 Q/R site, but edits efficiently at the R/G site and HOTSPOT1. Its viral RNA substrates include: hepatitis C virus (HCV), vesicular stomatitis virus (VSV), measles virus (MV), hepatitis delta virus (HDV), and human immunodeficiency virus type 1 (HIV-1). Exhibits either a proviral (HDV, MV, VSV and HIV-1) or an antiviral effect (HCV) and this can be editing-dependent (HDV and HCV), editing-independent (VSV and MV) or both (HIV-1). Impairs HCV replication via RNA editing at multiple sites. Enhances the replication of MV, VSV and HIV-1 through an editing- independent mechanism via suppression of EIF2AK2/PKR activation and function. Stimulates both the release and infectivity of HIV-1 viral particles by an editing-dependent mechanism where it associates with viral RNAs and edits adenosines in the 5'UTR and the Rev and Tat coding sequence. Can enhance viral replication of HDV via A-to-I editing at a site designated as amber/W, thereby changing an UAG amber stop codon to an UIG tryptophan (W) codon that permits synthesis of the large delta antigen (L-HDAg) which has a key role in the assembly of viral particles. However, high levels of ADAR1 inhibit HDV replication. {ECO:0000269|PubMed:12618436, ECO:0000269|PubMed:15556947, ECO:0000269|PubMed:15858013, ECO:0000269|PubMed:16120648, ECO:0000269|PubMed:16475990, ECO:0000269|PubMed:17079286, ECO:0000269|PubMed:19605474, ECO:0000269|PubMed:19651874, ECO:0000269|PubMed:19710021, ECO:0000269|PubMed:19908260, ECO:0000269|PubMed:21289159, ECO:0000269|PubMed:22278222, ECO:0000269|PubMed:7565688, ECO:0000269|PubMed:7972084}.; ",{"$nulls":4},"p.Pro3Ala","c.7C>G","MODERATE","3/1226",1,{"$nulls":5},"5","917","1229","640","812","487","692","0","0","0","0.1951",{"$nulls":20},"2.7271330000000003","2.79;.;.","0.69","1;1;0.997788","-0.9;.;.","0.734;0.734;0.827","0.031;.;.","0.315;.;.",{"$nulls":3},"Unknown",-1,"AD/AR","Dyschromatosis symmetrica hereditaria; Aicardi-Goutieres syndrome 6","Dermatologic; Hematologic; Neurologic",{"$nulls":3},"C3539013| C0406775","0/0","898,0","0","898","0/1","996,184","0.1559","1180",null,"chr1:154608000:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1564"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ANKRD34C","chr15:79293417","ANKRD34C(E45K)",{"$nulls":6},255,"PASS","Missense","rs779874764",-1,{"$nulls":6},"p.Glu45Lys","c.133G>A","MODERATE","45/535",1,1,{"$nulls":4},"5","358","221","293","175","296","181","0","0","0","0.3039",{"$nulls":20},"3.917021","-0.14","0.37","0.998575","-2.89","1.0","0.004","0.661",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","357,0","0","357","0/1","159,58","0.2673","217",null,"chr15:79293417:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2686"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ANKRD34C","chr15:79293417","ANKRD34C(E45K)",{"$nulls":6},255,"PASS","Missense","rs779874764",-1,{"$nulls":6},"p.Glu45Lys","c.133G>A","MODERATE","45/535",1,1,{"$nulls":4},"5","358","214","293","165","295","179","0","0","0","0.2849",{"$nulls":20},"3.917021","-0.14","0.37","0.998575","-2.89","1.0","0.004","0.661",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","362,0","0","362","0/1","152,56","0.2692","208",null,"chr15:79293417:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2545"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","APLNR","chr11:57236748","APLNR(A86V)",null,null,"transmembrane region (Helical; Name=2 ), helix ",{"$nulls":3},255,"PASS","Missense","rs994466745",-1,null,"FUNCTION: Receptor for apelin receptor early endogenous ligand (APELA) and apelin (APLN) hormones coupled to G proteins that inhibit adenylate cyclase activity (PubMed:11090199, PubMed:25639753, PubMed:28137936). Plays a key role in early development such as gastrulation, blood vessels formation and heart morphogenesis by acting as a receptor for APELA hormone (By similarity). May promote angioblast migration toward the embryonic midline, i.e. the position of the future vessel formation, during vasculogenesis (By similarity). Promotes sinus venosus (SV)- derived endothelial cells migration into the developing heart to promote coronary blood vessel development (By similarity). Plays also a role in various processes in adults such as regulation of blood vessel formation, blood pressure, heart contractility and heart failure (PubMed:25639753, PubMed:28137936). {ECO:0000250|UniProtKB:P79960, ECO:0000250|UniProtKB:Q7SZP9, ECO:0000250|UniProtKB:Q9WV08, ECO:0000269|PubMed:11090199, ECO:0000269|PubMed:25639753, ECO:0000269|PubMed:28137936}.; ",{"$nulls":4},"p.Ala86Val","c.257C>T","MODERATE","86/380",1,{"$nulls":5},"5","874","688","706","514","758","601","0","0","0","0.2629",{"$nulls":20},"4.115354",null,"1.835","0.999998",null,"1.0",null,"0.665;0.697",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","859,0","0","859","0/1","485,172","0.2618","657",null,"chr11:57236748:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2782"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","APLNR","chr11:57236748","APLNR(A86V)",null,null,"transmembrane region (Helical; Name=2 ), helix ",{"$nulls":3},255,"PASS","Missense","rs994466745",-1,null,"FUNCTION: Receptor for apelin receptor early endogenous ligand (APELA) and apelin (APLN) hormones coupled to G proteins that inhibit adenylate cyclase activity (PubMed:11090199, PubMed:25639753, PubMed:28137936). Plays a key role in early development such as gastrulation, blood vessels formation and heart morphogenesis by acting as a receptor for APELA hormone (By similarity). May promote angioblast migration toward the embryonic midline, i.e. the position of the future vessel formation, during vasculogenesis (By similarity). Promotes sinus venosus (SV)- derived endothelial cells migration into the developing heart to promote coronary blood vessel development (By similarity). Plays also a role in various processes in adults such as regulation of blood vessel formation, blood pressure, heart contractility and heart failure (PubMed:25639753, PubMed:28137936). {ECO:0000250|UniProtKB:P79960, ECO:0000250|UniProtKB:Q7SZP9, ECO:0000250|UniProtKB:Q9WV08, ECO:0000269|PubMed:11090199, ECO:0000269|PubMed:25639753, ECO:0000269|PubMed:28137936}.; ",{"$nulls":4},"p.Ala86Val","c.257C>T","MODERATE","86/380",1,{"$nulls":5},"5","874","612","706","455","757","517","0","0","0","0.3849",{"$nulls":20},"4.115354",null,"1.835","0.999998",null,"1.0",null,"0.665;0.697",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","871,0","0","871","0/1","367,229","0.3842","596",null,"chr11:57236748:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3868"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","AR","chrX:67711566","AR(G684S)",null,null,"domain (NR LBD ), region of interest (Interaction with LPXN ), region of interest (Interaction with CCAR1 ), region of interest (Interaction with KAT7 ), splice variant (In isoform 3. ), splice variant (In isoform 4. ), sequence variant (In prostate cancer. AR(G684A))",{"$nulls":3},255,"PASS","Missense","rs1020357614",-1,"DISEASE: Androgen insensitivity syndrome (AIS) [MIM:300068]: An X- linked recessive form of pseudohermaphroditism due end-organ resistance to androgen. Affected males have female external genitalia, female breast development, blind vagina, absent uterus and female adnexa, and abdominal or inguinal testes, despite a normal 46,XY karyotype. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10221770, ECO:0000269|PubMed:10404311, ECO:0000269|PubMed:10458483, ECO:0000269|PubMed:10571951, ECO:0000269|PubMed:10590024, ECO:0000269|PubMed:10690872, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:11744994, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1426313, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:1464650, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:1480178, ECO:0000269|PubMed:1487249, ECO:0000269|PubMed:1569163, ECO:0000269|PubMed:1609793, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:16595706, ECO:0000269|PubMed:1775137, ECO:0000269|PubMed:1999491, ECO:0000269|PubMed:2082179, ECO:0000269|PubMed:2594783, ECO:0000269|PubMed:7537149, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7633398, ECO:0000269|PubMed:7641413, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7962294, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:7981689, ECO:0000269|PubMed:7993455, ECO:0000269|PubMed:8040309, ECO:0000269|PubMed:8096390, ECO:0000269|PubMed:8103398, ECO:0000269|PubMed:8162033, ECO:0000269|PubMed:8224266, ECO:0000269|PubMed:8281140, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8339746, ECO:0000269|PubMed:8413310, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8626869, ECO:0000269|PubMed:8647313, ECO:0000269|PubMed:8683794, ECO:0000269|PubMed:8723113, ECO:0000269|PubMed:8768864, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8830623, ECO:0000269|PubMed:8918984, ECO:0000269|PubMed:8990010, ECO:0000269|PubMed:9001799, ECO:0000269|PubMed:9007482, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9106550, ECO:0000269|PubMed:9160185, ECO:0000269|PubMed:9252933, ECO:0000269|PubMed:9255042, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9328206, ECO:0000269|PubMed:9544375, ECO:0000269|PubMed:9554754, ECO:0000269|PubMed:9610419, ECO:0000269|PubMed:9627582, ECO:0000269|PubMed:9698822, ECO:0000269|PubMed:9851768, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.113, ECO:0000269|Ref.179}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinal and bulbar muscular atrophy X-linked 1 (SMAX1) [MIM:313200]: An X-linked recessive form of spinal muscular atrophy. Spinal muscular atrophy refers to a group of neuromuscular disorders characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMAX1 occurs only in men. Age at onset is usually in the third to fifth decade of life, but earlier involvement has been reported. It is characterized by slowly progressive limb and bulbar muscle weakness with fasciculations, muscle atrophy, and gynecomastia. The disorder is clinically similar to classic forms of autosomal spinal muscular atrophy. {ECO:0000269|PubMed:15851746}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by trinucleotide CAG repeat expansion. In SMAX1 patients the number of Gln ranges from 38 to 62. Longer expansions result in earlier onset and more severe clinical manifestations of the disease.; DISEASE: Note=Defects in AR may play a role in metastatic prostate cancer. The mutated receptor stimulates prostate growth and metastases development despite of androgen ablation. This treatment can reduce primary and metastatic lesions probably by inducing apoptosis of tumor cells when they express the wild-type receptor. {ECO:0000269|PubMed:10363963, ECO:0000269|PubMed:10569618, ECO:0000269|PubMed:1562539, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:17311914, ECO:0000269|PubMed:2260966, ECO:0000269|PubMed:25091737, ECO:0000269|PubMed:8187068, ECO:0000269|PubMed:8274409, ECO:0000269|PubMed:8827083}.; DISEASE: Androgen insensitivity, partial (PAIS) [MIM:312300]: A disorder that is characterized by hypospadias, hypogonadism, gynecomastia, genital ambiguity, normal XY karyotype, and a pedigree pattern consistent with X-linked recessive inheritance. Some patients present azoospermia or severe oligospermia without other clinical manifestations. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10470409, ECO:0000269|PubMed:10502786, ECO:0000269|PubMed:10543676, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:1303262, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1424203, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:2010552, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7649358, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7909256, ECO:0000269|PubMed:7910529, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:8033918, ECO:0000269|PubMed:8097257, ECO:0000269|PubMed:8126121, ECO:0000269|PubMed:8205256, ECO:0000269|PubMed:8281139, ECO:0000269|PubMed:8325932, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8550758, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8823308, ECO:0000269|PubMed:8824883, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9196614, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9329414, ECO:0000269|PubMed:9543136, ECO:0000269|PubMed:9607727, ECO:0000269|PubMed:9768671, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.121}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Steroid hormone receptors are ligand-activated transcription factors that regulate eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Transcription factor activity is modulated by bound coactivator and corepressor proteins like ZBTB7A that recruits NCOR1 and NCOR2 to the androgen response elements/ARE on target genes, negatively regulating androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Transcription activation is also down-regulated by NR0B2. Activated, but not phosphorylated, by HIPK3 and ZIPK/DAPK3. {ECO:0000269|PubMed:14664718, ECO:0000269|PubMed:15563469, ECO:0000269|PubMed:17591767, ECO:0000269|PubMed:17911242, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:19345326, ECO:0000269|PubMed:20812024, ECO:0000269|PubMed:20980437, ECO:0000269|PubMed:25091737}.; ","gedi|foundationOne|level2","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","p.Gly684Ser","c.2050G>A","MODERATE","684/920",4,{"$nulls":5},"4","1016","600","763","451","868","517","0","0","0","0.2321",{"$nulls":20},"3.226748",".;-2.24;-6.62;-6.62",null,"0.979248",".;-0.59;-0.15;-0.31",null,".;0.235;0.134;0.009","0.324;0.263;0.281;0.236",{"$nulls":3},"Unknown",-1,"XL","Androgen insensitivity; Androgen insensitivity, partial","Endocrine; Genitourinary; Neurologic; Oncologic","kCANCER",null,null,"C0039585| C0268301| C2678098| C1839259| C0376358","0/0","978,0","0","978","0/1","440,127","0.224","567",null,"chrX:67711566:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2173"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","AR","chrX:67711566","AR(G684S)",null,null,"domain (NR LBD ), region of interest (Interaction with LPXN ), region of interest (Interaction with CCAR1 ), region of interest (Interaction with KAT7 ), splice variant (In isoform 3. ), splice variant (In isoform 4. ), sequence variant (In prostate cancer. AR(G684A))",{"$nulls":3},255,"PASS","Missense","rs1020357614",-1,"DISEASE: Androgen insensitivity syndrome (AIS) [MIM:300068]: An X- linked recessive form of pseudohermaphroditism due end-organ resistance to androgen. Affected males have female external genitalia, female breast development, blind vagina, absent uterus and female adnexa, and abdominal or inguinal testes, despite a normal 46,XY karyotype. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10221770, ECO:0000269|PubMed:10404311, ECO:0000269|PubMed:10458483, ECO:0000269|PubMed:10571951, ECO:0000269|PubMed:10590024, ECO:0000269|PubMed:10690872, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:11744994, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1426313, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:1464650, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:1480178, ECO:0000269|PubMed:1487249, ECO:0000269|PubMed:1569163, ECO:0000269|PubMed:1609793, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:16595706, ECO:0000269|PubMed:1775137, ECO:0000269|PubMed:1999491, ECO:0000269|PubMed:2082179, ECO:0000269|PubMed:2594783, ECO:0000269|PubMed:7537149, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7633398, ECO:0000269|PubMed:7641413, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7962294, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:7981689, ECO:0000269|PubMed:7993455, ECO:0000269|PubMed:8040309, ECO:0000269|PubMed:8096390, ECO:0000269|PubMed:8103398, ECO:0000269|PubMed:8162033, ECO:0000269|PubMed:8224266, ECO:0000269|PubMed:8281140, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8339746, ECO:0000269|PubMed:8413310, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8626869, ECO:0000269|PubMed:8647313, ECO:0000269|PubMed:8683794, ECO:0000269|PubMed:8723113, ECO:0000269|PubMed:8768864, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8830623, ECO:0000269|PubMed:8918984, ECO:0000269|PubMed:8990010, ECO:0000269|PubMed:9001799, ECO:0000269|PubMed:9007482, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9106550, ECO:0000269|PubMed:9160185, ECO:0000269|PubMed:9252933, ECO:0000269|PubMed:9255042, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9328206, ECO:0000269|PubMed:9544375, ECO:0000269|PubMed:9554754, ECO:0000269|PubMed:9610419, ECO:0000269|PubMed:9627582, ECO:0000269|PubMed:9698822, ECO:0000269|PubMed:9851768, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.113, ECO:0000269|Ref.179}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinal and bulbar muscular atrophy X-linked 1 (SMAX1) [MIM:313200]: An X-linked recessive form of spinal muscular atrophy. Spinal muscular atrophy refers to a group of neuromuscular disorders characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMAX1 occurs only in men. Age at onset is usually in the third to fifth decade of life, but earlier involvement has been reported. It is characterized by slowly progressive limb and bulbar muscle weakness with fasciculations, muscle atrophy, and gynecomastia. The disorder is clinically similar to classic forms of autosomal spinal muscular atrophy. {ECO:0000269|PubMed:15851746}. Note=The disease is caused by mutations affecting the gene represented in this entry. Caused by trinucleotide CAG repeat expansion. In SMAX1 patients the number of Gln ranges from 38 to 62. Longer expansions result in earlier onset and more severe clinical manifestations of the disease.; DISEASE: Note=Defects in AR may play a role in metastatic prostate cancer. The mutated receptor stimulates prostate growth and metastases development despite of androgen ablation. This treatment can reduce primary and metastatic lesions probably by inducing apoptosis of tumor cells when they express the wild-type receptor. {ECO:0000269|PubMed:10363963, ECO:0000269|PubMed:10569618, ECO:0000269|PubMed:1562539, ECO:0000269|PubMed:16129672, ECO:0000269|PubMed:17311914, ECO:0000269|PubMed:2260966, ECO:0000269|PubMed:25091737, ECO:0000269|PubMed:8187068, ECO:0000269|PubMed:8274409, ECO:0000269|PubMed:8827083}.; DISEASE: Androgen insensitivity, partial (PAIS) [MIM:312300]: A disorder that is characterized by hypospadias, hypogonadism, gynecomastia, genital ambiguity, normal XY karyotype, and a pedigree pattern consistent with X-linked recessive inheritance. Some patients present azoospermia or severe oligospermia without other clinical manifestations. {ECO:0000269|PubMed:10022458, ECO:0000269|PubMed:10221692, ECO:0000269|PubMed:10470409, ECO:0000269|PubMed:10502786, ECO:0000269|PubMed:10543676, ECO:0000269|PubMed:11587068, ECO:0000269|PubMed:1303262, ECO:0000269|PubMed:1307250, ECO:0000269|PubMed:1316540, ECO:0000269|PubMed:1424203, ECO:0000269|PubMed:1430233, ECO:0000269|PubMed:14756668, ECO:0000269|PubMed:2010552, ECO:0000269|PubMed:7581399, ECO:0000269|PubMed:7649358, ECO:0000269|PubMed:7671849, ECO:0000269|PubMed:7909256, ECO:0000269|PubMed:7910529, ECO:0000269|PubMed:7929841, ECO:0000269|PubMed:7970939, ECO:0000269|PubMed:7981687, ECO:0000269|PubMed:8033918, ECO:0000269|PubMed:8097257, ECO:0000269|PubMed:8126121, ECO:0000269|PubMed:8205256, ECO:0000269|PubMed:8281139, ECO:0000269|PubMed:8325932, ECO:0000269|PubMed:8325950, ECO:0000269|PubMed:8446106, ECO:0000269|PubMed:8550758, ECO:0000269|PubMed:8809734, ECO:0000269|PubMed:8823308, ECO:0000269|PubMed:8824883, ECO:0000269|PubMed:9039340, ECO:0000269|PubMed:9196614, ECO:0000269|PubMed:9302173, ECO:0000269|PubMed:9329414, ECO:0000269|PubMed:9543136, ECO:0000269|PubMed:9607727, ECO:0000269|PubMed:9768671, ECO:0000269|PubMed:9856504, ECO:0000269|Ref.121}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Steroid hormone receptors are ligand-activated transcription factors that regulate eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Transcription factor activity is modulated by bound coactivator and corepressor proteins like ZBTB7A that recruits NCOR1 and NCOR2 to the androgen response elements/ARE on target genes, negatively regulating androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Transcription activation is also down-regulated by NR0B2. Activated, but not phosphorylated, by HIPK3 and ZIPK/DAPK3. {ECO:0000269|PubMed:14664718, ECO:0000269|PubMed:15563469, ECO:0000269|PubMed:17591767, ECO:0000269|PubMed:17911242, ECO:0000269|PubMed:18084323, ECO:0000269|PubMed:19345326, ECO:0000269|PubMed:20812024, ECO:0000269|PubMed:20980437, ECO:0000269|PubMed:25091737}.; ","gedi|foundationOne|level2","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","[ \"Bicalutamide\" , \"Enzalutamide\" , \"Flutamide\" , \"Nilutamide\"]","p.Gly684Ser","c.2050G>A","MODERATE","684/920",4,{"$nulls":5},"4","1016","494","763","363","868","432","0","0","0","0.3542",{"$nulls":20},"3.226748",".;-2.24;-6.62;-6.62",null,"0.979248",".;-0.59;-0.15;-0.31",null,".;0.235;0.134;0.009","0.324;0.263;0.281;0.236",{"$nulls":3},"Unknown",-1,"XL","Androgen insensitivity; Androgen insensitivity, partial","Endocrine; Genitourinary; Neurologic; Oncologic","kCANCER",null,null,"C0039585| C0268301| C2678098| C1839259| C0376358","0/0","990,0","0","990","0/1","317,157","0.3312","474",null,"chrX:67711566:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3388"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ARMC2","chr6:108899741","ARMC2(E266K)",{"$nulls":6},255,"PASS","Missense","rs6911885",0.0003995,{"$nulls":6},"p.Glu266Lys","c.796G>A","MODERATE","266/867",7,2,{"$nulls":4},"5","140","174","101","116","121","151","0","0","0","0.1523",{"$nulls":20},"3.2531280000000002","0.47",".;2.155","0.782788;0.829578","-0.27;-0.36",".;0.272","0.495;0.612","0.244;0.25",{"$nulls":3},"ExAC_AFR_AF",0.0003995,{"$nulls":6},"C5193095","0/0","137,0","0","137","0/1","142,27","0.1598","169",null,"chr6:108899741:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1552"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ARMC2","chr6:108899741","ARMC2(E266K)",{"$nulls":6},255,"PASS","Missense","rs6911885",0.0003995,{"$nulls":6},"p.Glu266Lys","c.796G>A","MODERATE","266/867",7,2,{"$nulls":4},"5","140","223","101","149","121","191","0","0","0","0.2565",{"$nulls":20},"3.2531280000000002","0.47",".;2.155","0.782788;0.829578","-0.27;-0.36",".;0.272","0.495;0.612","0.244;0.25",{"$nulls":3},"ExAC_AFR_AF",0.0003995,{"$nulls":6},"C5193095","0/0","136,0","0","136","0/1","156,54","0.2571","210",null,"chr6:108899741:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2617"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","BIRC2","chr11:102350096","BIRC2(V81G)",null,null,"repeat (BIR 1 ), strand ","beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Multi-functional protein which regulates not only caspases and apoptosis, but also modulates inflammatory signaling and immunity, mitogenic kinase signaling, and cell proliferation, as well as cell invasion and metastasis. Acts as an E3 ubiquitin- protein ligase regulating NF-kappa-B signaling and regulates both canonical and non-canonical NF-kappa-B signaling by acting in opposite directions: acts as a positive regulator of the canonical pathway and suppresses constitutive activation of non-canonical NF-kappa-B signaling. The target proteins for its E3 ubiquitin- protein ligase activity include: RIPK1, RIPK2, RIPK3, RIPK4, CASP3, CASP7, CASP8, TRAF2, DIABLO/SMAC, MAP3K14/NIK, MAP3K5/ASK1, IKBKG/NEMO, IKBKE and MXD1/MAD1. Can also function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway, targeting effector caspases for neddylation and inactivation. Acts as an important regulator of innate immune signaling via regulation of Toll-like receptors (TLRs), Nodlike receptors (NLRs) and RIG-I like receptors (RLRs), collectively referred to as pattern recognition receptors (PRRs). Protects cells from spontaneous formation of the ripoptosome, a large multi-protein complex that has the capability to kill cancer cells in a caspase- dependent and caspase-independent manner. Suppresses ripoptosome formation by ubiquitinating RIPK1 and CASP8. Can stimulate the transcriptional activity of E2F1. Plays a role in the modulation of the cell cycle. {ECO:0000269|PubMed:15665297, ECO:0000269|PubMed:18082613, ECO:0000269|PubMed:21145488, ECO:0000269|PubMed:21653699, ECO:0000269|PubMed:21931591, ECO:0000269|PubMed:23453969}.; ","level2",{"$nulls":3},"p.Val81Gly","c.242T>G","MODERATE","81/618",2,{"$nulls":5},"5","550","439","425","336","488","389","0","0","0","0.2853",{"$nulls":20},"4.149115","2.88;2.88;2.88;2.88;.;.",".;3.52;.;.;.;3.52","1","-5.44;-5.68;-5.68;-6.88;.;.",".;1.0;.;.;.;1.0","0.0;0.0;0.0;0.0;.;.","0.734;0.722;0.732;.;.;0.725",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS,kCANCER",{"$nulls":3},"0/0","543,0","0","543","0/1","305,126","0.2923","431",null,"chr11:102350096:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2827"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","BIRC2","chr11:102350096","BIRC2(V81G)",null,null,"repeat (BIR 1 ), strand ","beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Multi-functional protein which regulates not only caspases and apoptosis, but also modulates inflammatory signaling and immunity, mitogenic kinase signaling, and cell proliferation, as well as cell invasion and metastasis. Acts as an E3 ubiquitin- protein ligase regulating NF-kappa-B signaling and regulates both canonical and non-canonical NF-kappa-B signaling by acting in opposite directions: acts as a positive regulator of the canonical pathway and suppresses constitutive activation of non-canonical NF-kappa-B signaling. The target proteins for its E3 ubiquitin- protein ligase activity include: RIPK1, RIPK2, RIPK3, RIPK4, CASP3, CASP7, CASP8, TRAF2, DIABLO/SMAC, MAP3K14/NIK, MAP3K5/ASK1, IKBKG/NEMO, IKBKE and MXD1/MAD1. Can also function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway, targeting effector caspases for neddylation and inactivation. Acts as an important regulator of innate immune signaling via regulation of Toll-like receptors (TLRs), Nodlike receptors (NLRs) and RIG-I like receptors (RLRs), collectively referred to as pattern recognition receptors (PRRs). Protects cells from spontaneous formation of the ripoptosome, a large multi-protein complex that has the capability to kill cancer cells in a caspase- dependent and caspase-independent manner. Suppresses ripoptosome formation by ubiquitinating RIPK1 and CASP8. Can stimulate the transcriptional activity of E2F1. Plays a role in the modulation of the cell cycle. {ECO:0000269|PubMed:15665297, ECO:0000269|PubMed:18082613, ECO:0000269|PubMed:21145488, ECO:0000269|PubMed:21653699, ECO:0000269|PubMed:21931591, ECO:0000269|PubMed:23453969}.; ","level2",{"$nulls":3},"p.Val81Gly","c.242T>G","MODERATE","81/618",2,{"$nulls":5},"5","550","455","425","344","487","389","0","0","0","0.3599",{"$nulls":20},"4.149115","2.88;2.88;2.88;2.88;.;.",".;3.52;.;.;.;3.52","1","-5.44;-5.68;-5.68;-6.88;.;.",".;1.0;.;.;.;1.0","0.0;0.0;0.0;0.0;.;.","0.734;0.722;0.732;.;.;0.725",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kAPOPTOSIS,kCANCER",{"$nulls":3},"0/0","543,0","0","543","0/1","287,155","0.3507","442",null,"chr11:102350096:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3488"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","BPIFB2","chr20:33018330","BPIFB2(Y217H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Tyr217His","c.649T>C","MODERATE","217/458",8,{"$nulls":5},"5","697","744","483","495","650","683","0","0","0","0.0747",{"$nulls":20},"1.9393880000000001","3.17","1.67","0.999831","-2.25","0.004","0.222","0.351",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","686,0","0","686","0/1","642,66","0.0932","708",null,"chr20:33018330:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0949"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","C10orf71","chr10:49323014","C10orf71(R157S)",{"$nulls":6},255,"PASS","Missense","rs754197819",-1,null,"FUNCTION: Plays an important role in cardiomyocyte hypertrophy via activation of the calcineurin/NFAT signaling pathway. {ECO:0000250|UniProtKB:M0RD54}.; ",{"$nulls":4},"p.Arg157Ser","c.469C>A","MODERATE","157/1435",3,{"$nulls":5},"5","367","288","288","224","321","255","0","0","0","0.098",{"$nulls":20},"0.906956","3.64",null,"1","-1.49",null,"0.394","0.053",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","258,28","0.0979","286",null,"chr10:49323014:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1116"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","C10orf71","chr10:49323014","C10orf71(R157S)",{"$nulls":6},255,"PASS","Missense","rs754197819",-1,null,"FUNCTION: Plays an important role in cardiomyocyte hypertrophy via activation of the calcineurin/NFAT signaling pathway. {ECO:0000250|UniProtKB:M0RD54}.; ",{"$nulls":4},"p.Arg157Ser","c.469C>A","MODERATE","157/1435",3,{"$nulls":5},"5","367","287","288","228","320","251","0","0","0","0.1474",{"$nulls":20},"0.906956","3.64",null,"1","-1.49",null,"0.394","0.053",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","239,44","0.1555","283",null,"chr10:49323014:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1754"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","C11orf74","chr11:36636119","C11orf74(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":7},"c.358+2T>C","HIGH",null,4,{"$nulls":5},"5","532","448","353","284","503","413","0","0","0","0.092",{"$nulls":5},"(C11orf74|ENSG00000166352|1|1.00)",{"$nulls":14},"4.457124",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","523,0","0","523","0/1","371,45","0.1082","416",null,"chr11:36636119:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1021"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","C5","chr9:121006915","C5(I804S)",null,null,"disulfide bond , strand ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Complement component 5 deficiency (C5D) [MIM:609536]: A rare defect of the complement classical pathway associated with susceptibility to severe recurrent infections, predominantly by Neisseria gonorrhoeae or Neisseria meningitidis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=An association study of C5 haplotypes and genotypes in individuals with chronic hepatitis C virus infection shows that individuals homozygous for the C5_1 haplotype have a significantly higher stage of liver fibrosis than individuals carrying at least 1 other allele. {ECO:0000269|PubMed:15995705}.; ","FUNCTION: Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled.; ",{"$nulls":4},"p.Ile804Ser","c.2411T>G","MODERATE","804/1676",19,{"$nulls":5},"5","412","499","295","348","348","420","0","0","0","0.1238",{"$nulls":20},"4.045608","1.68","2.475","0.999917","-4.17","0.999","0.002","0.872",{"$nulls":3},"Unknown",-1,"AD/AR"," Eculizumab, poor response to; Complement component 5 deficiency","Craniofacial; Musculoskeletal; Neurologic",null,"The protein encoded by this gene is the fifth component of complement, which plays an important role in inflammatory and cell killing processes. This protein is comprised of alpha and beta polypeptide chains that are linked by a disulfide bridge. An activation peptide, C5a, which is an anaphylatoxin that possesses potent spasmogenic and chemotactic activity, is derived from the alpha polypeptide via cleavage with a convertase. The C5b macromolecular cleavage product can form a complex with the C6 complement component, and this complex is the basis for formation of the membrane attack complex, which includes additional complement components. Mutations in this gene cause complement component 5 deficiency, a disease where patients show a propensity for severe recurrent infections. Defects in this gene have also been linked to a susceptibility to liver fibrosis and to rheumatoid arthritis. [provided by RefSeq, Jul 2008].  ",null,"C0343047| C3810402","0/0","403,0","0","403","0/1","417,52","0.1109","469",null,"chr9:121006915:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1178"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","CHTF18","chr16:792532","CHTF18(R669W)",{"$nulls":6},255,"PASS","Missense","rs369025596",0.0003762,null,"FUNCTION: Chromosome cohesion factor involved in sister chromatid cohesion and fidelity of chromosome transmission. Component of one of the cell nuclear antigen loader complexes, CTF18-replication factor C (CTF18-RFC), which consists of CTF18, CTF8, DCC1, RFC2, RFC3, RFC4 and RFC5. The CTF18-RFC complex binds to single- stranded and primed DNAs and has weak ATPase activity that is stimulated by the presence of primed DNA, replication protein A (RPA) and by proliferating cell nuclear antigen (PCNA). The CTF18- RFC complex catalyzes the ATP-dependent loading of PCNA onto primed and gapped DNA. It also interacts with and stimulates DNA polymerase POLH. {ECO:0000269|PubMed:12766176, ECO:0000269|PubMed:12930902, ECO:0000269|PubMed:17545166}.; ",{"$nulls":4},"p.Arg669Trp","c.2005C>T","MODERATE","669/1184",12,1,{"$nulls":4},"5","526","389","422","313","427","314","0","0","0","0.3344",{"$nulls":20},"2.895949",".;2.85;2.85;.",".;2.685;.;.","1",".;-5.01;-5.01;.",".;1.0;1.0;.",".;0.004;0.003;.","0.37;0.413;0.379;0.413",{"$nulls":3},"ExAC_SAS_AF",0.0003762,{"$nulls":7},"0/0","516,0","0","516","0/1","255,125","0.3289","380",null,"chr16:792532:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3291"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","CHTF18","chr16:792532","CHTF18(R669W)",{"$nulls":6},255,"PASS","Missense","rs369025596",0.0003762,null,"FUNCTION: Chromosome cohesion factor involved in sister chromatid cohesion and fidelity of chromosome transmission. Component of one of the cell nuclear antigen loader complexes, CTF18-replication factor C (CTF18-RFC), which consists of CTF18, CTF8, DCC1, RFC2, RFC3, RFC4 and RFC5. The CTF18-RFC complex binds to single- stranded and primed DNAs and has weak ATPase activity that is stimulated by the presence of primed DNA, replication protein A (RPA) and by proliferating cell nuclear antigen (PCNA). The CTF18- RFC complex catalyzes the ATP-dependent loading of PCNA onto primed and gapped DNA. It also interacts with and stimulates DNA polymerase POLH. {ECO:0000269|PubMed:12766176, ECO:0000269|PubMed:12930902, ECO:0000269|PubMed:17545166}.; ",{"$nulls":4},"p.Arg669Trp","c.2005C>T","MODERATE","669/1184",12,1,{"$nulls":4},"5","526","318","422","261","427","253","0","0","0","0.3676",{"$nulls":20},"2.895949",".;2.85;2.85;.",".;2.685;.;.","1",".;-5.01;-5.01;.",".;1.0;1.0;.",".;0.004;0.003;.","0.37;0.413;0.379;0.413",{"$nulls":3},"ExAC_SAS_AF",0.0003762,{"$nulls":7},"0/0","516,0","0","516","0/1","197,116","0.3706","313",null,"chr16:792532:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3678"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","CISD1","chr10:58287597","CISD1(E92Q)",null,null,"topological domain (Cytoplasmic ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a key role in regulating maximal capacity for electron transport and oxidative phosphorylation (By similarity). May be involved in Fe-S cluster shuttling and/or in redox reactions. {ECO:0000250, ECO:0000269|PubMed:17584744, ECO:0000269|PubMed:17766440}.; ",{"$nulls":4},"p.Glu92Gln","c.274G>C","MODERATE","92/108",3,{"$nulls":5},"5","148","92","102","60","139","85","0","0","0","0.1176",{"$nulls":20},"2.81068",null,"1.675","0.964242","-2.11","0.497","0.107","0.157",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","148,0","0","148","0/1","78,12","0.1333","90",null,"chr10:58287597:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1167"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","CISD1","chr10:58287597","CISD1(E92Q)",null,null,"topological domain (Cytoplasmic ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a key role in regulating maximal capacity for electron transport and oxidative phosphorylation (By similarity). May be involved in Fe-S cluster shuttling and/or in redox reactions. {ECO:0000250, ECO:0000269|PubMed:17584744, ECO:0000269|PubMed:17766440}.; ",{"$nulls":4},"p.Glu92Gln","c.274G>C","MODERATE","92/108",3,{"$nulls":5},"5","148","136","102","95","139","127","0","0","0","0.1811",{"$nulls":20},"2.81068",null,"1.675","0.964242","-2.11","0.497","0.107","0.157",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","149,0","0","149","0/1","110,24","0.1791","134",null,"chr10:58287597:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1684"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","DNAH3","chr16:21141336","DNAH3(M158_K161del)",null,null,"region of interest (Stem )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Involved in sperm motility; implicated in sperm flagellar assembly (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met158_Lys161del","c.473_484delTGAGGAAAAAAA","MODERATE","158/4116",4,{"$nulls":5},"4","344","316","232","206","262","236","0","0","0","0.1186",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","330,0","0","330","0/1","254,34","0.1181","288",null,"chr16:21141336:GTTTTTTTCCTCA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1311"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","EFCAB2","chr1:245121934","EFCAB2(R266C)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs560603203",9.9403578528827028E-4,null,"FUNCTION: Component of the nexin-dynein regulatory complex (N- DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. {ECO:0000250|UniProtKB:A8J3A0}.; ",{"$nulls":4},"p.Arg266Cys","c.796C>T","MODERATE","266/269",8,{"$nulls":5},"5","48","68","42","52","41","57","0","0","0","0.1228",{"$nulls":20},"1.056763","-1.35;-1.45",null,"1","-0.62;-0.65","0.0;.","0.0","0.057;0.152",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,{"$nulls":7},"0/0","48,0","0","48","0/1","57,10","0.1493","67",null,"chr1:245121934:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1538"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","EFCAB2","chr1:245121934","EFCAB2(R266C)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs560603203",9.9403578528827028E-4,null,"FUNCTION: Component of the nexin-dynein regulatory complex (N- DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. {ECO:0000250|UniProtKB:A8J3A0}.; ",{"$nulls":4},"p.Arg266Cys","c.796C>T","MODERATE","266/269",8,{"$nulls":5},"5","48","78","42","60","41","64","0","0","0","0.1562",{"$nulls":20},"1.056763","-1.35;-1.45",null,"1","-0.62;-0.65","0.0;.","0.0","0.057;0.152",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,{"$nulls":7},"0/0","48,0","0","48","0/1","63,14","0.1818","77",null,"chr1:245121934:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1833"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","EPB41L3","chr18:5416140","EPB41L3(G582V)",null,null,"region of interest (Spectrin--actin-binding ), splice variant (In isoform 2, isoform 3 and isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Tumor suppressor that inhibits cell proliferation and promotes apoptosis. Modulates the activity of protein arginine N- methyltransferases, including PRMT3 and PRMT5. {ECO:0000269|PubMed:15334060, ECO:0000269|PubMed:15737618, ECO:0000269|PubMed:16420693, ECO:0000269|PubMed:9892180}.; ",{"$nulls":4},"p.Gly582Val","c.1745G>T","MODERATE","582/1087",13,{"$nulls":5},"5","436","358","336","294","374","320","0","0","0","0.1313",{"$nulls":20},"3.4037290000000002","-1.63","2.295","1","-1.7","0.993","0.002","0.591",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","430,0","0","430","0/1","312,49","0.1357","361",null,"chr18:5416140:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1224"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","EPB41L3","chr18:5416140","EPB41L3(G582V)",null,null,"region of interest (Spectrin--actin-binding ), splice variant (In isoform 2, isoform 3 and isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Tumor suppressor that inhibits cell proliferation and promotes apoptosis. Modulates the activity of protein arginine N- methyltransferases, including PRMT3 and PRMT5. {ECO:0000269|PubMed:15334060, ECO:0000269|PubMed:15737618, ECO:0000269|PubMed:16420693, ECO:0000269|PubMed:9892180}.; ",{"$nulls":4},"p.Gly582Val","c.1745G>T","MODERATE","582/1087",13,{"$nulls":5},"5","436","401","336","315","372","355","0","0","0","0.1183",{"$nulls":20},"3.4037290000000002","-1.63","2.295","1","-1.7","0.993","0.002","0.591",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","430,0","0","430","0/1","340,49","0.126","389",null,"chr18:5416140:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.127"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","FARP1","chr13:98388381","FARP1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Functions as guanine nucleotide exchange factor for RAC1. May play a role in semaphorin signaling. Plays a role in the assembly and disassembly of dendritic filopodia, the formation of dendritic spines, regulation of dendrite length and ultimately the formation of synapses (By similarity). {ECO:0000250}.; ",{"$nulls":5},"c.760-2A>T","HIGH",null,8,{"$nulls":5},"5","356","232","275","176","309","199","0","0","0","0.1005",{"$nulls":5},"(FARP1|ENSG00000152767|1|1.00)",{"$nulls":14},"6.214862",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","355,0","0","355","0/1","204,23","0.1013","227",null,"chr13:98388381:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1023"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","FGD3","chr9:93006088","FGD3(E249K)",null,null,"domain (DH )",{"$nulls":3},255,"PASS","Missense","rs550953081",9.9403578528827028E-4,null,"FUNCTION: Promotes the formation of filopodia. May activate CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu249Lys","c.745G>A","MODERATE","249/725",6,1,{"$nulls":4},"5","861","912","620","624","779","797","0","0","0","0.1907",{"$nulls":20},"4.277681","-0.06;-0.06;.;-0.06","2.18","1","-3.82;-3.82;.;-3.82","1.0;.;1.0;1.0","0.002;0.003;.;0.002","0.83;0.831;.;0.827",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,{"$nulls":7},"0/0","825,0","0","825","0/1","689,168","0.196","857",null,"chr9:93006088:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1955"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","FLNC","chr7:128848703","FLNC(T1575A)",null,null,"repeat (Filamin 14 ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Myopathy, myofibrillar, 5 (MFM5) [MIM:609524]: A form of myofibrillar myopathy, a group of chronic neuromuscular disorders characterized at ultrastructural level by disintegration of the sarcomeric Z disk and myofibrils, and replacement of the normal myofibrillar markings by small dense granules, or larger hyaline masses, or amorphous material. MFM5 is characterized by onset in adulthood, clinical features of a limb-girdle myopathy, and focal myofibrillar destruction. {ECO:0000269|PubMed:15929027}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Myopathy, distal, 4 (MPD4) [MIM:614065]: A slowly progressive muscular disorder characterized by distal muscle weakness and atrophy affecting the upper and lower limbs. Onset occurs around the third to fourth decades of life, and patients remain ambulatory even after long disease duration. Muscle biopsy shows non-specific changes with no evidence of rods, necrosis, or inflammation. {ECO:0000269|PubMed:21620354}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 26 (CMH26) [MIM:617047]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:25351925}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial restrictive 5 (RCM5) [MIM:617047]: A heart disorder characterized by impaired filling of the ventricles with reduced diastolic volume, in the presence of normal or near normal wall thickness and systolic function. {ECO:0000269|PubMed:26666891}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Muscle-specific filamin, which plays a central role in muscle cells, probably by functioning as a large actin-cross- linking protein. May be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. Critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers.; ","level2",{"$nulls":3},"p.Thr1575Ala","c.4723A>G","MODERATE","1575/2725",27,{"$nulls":5},"5","593","410","477","321","493","333","0","0","0","0.1261",{"$nulls":20},"1.688822","-1.84","0.4","0.999955","0.29;0.13","0.0;0.998","0.764;0.977","0.155;0.144",{"$nulls":3},"Unknown",-1,"AD","Myopathy, distal, 4; Myopathy, myofibrillar, 5","Cardiovascular; Musculoskeletal","kMAPK","This gene encodes one of three related filamin genes, specifically gamma filamin. These filamin proteins crosslink actin filaments into orthogonal networks in cortical cytoplasm and participate in the anchoring of membrane proteins for the actin cytoskeleton. Three functional domains exist in filamin: an N-terminal filamentous actin-binding domain, a C-terminal self-association domain, and a membrane glycoprotein-binding domain. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].",null,"C1836050| C3279722| C4310749","0/0","586,0","0","586","0/1","352,44","0.1111","396",null,"chr7:128848703:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1184"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","FLRT1","chr11:64116496","FLRT1(A77T)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs770193280",1.515E-4,null,"FUNCTION: Plays a role in fibroblast growth factor-mediated signaling cascades that lead to the activation of MAP kinases. Promotes neurite outgrowth via FGFR1-mediated activation of downstream MAP kinases. Promotes an increase both in neurite number and in neurite length. May play a role in cell-cell adhesion and cell guidance via its interaction with ADGRL1/LPHN1 and ADGRL3. {ECO:0000250|UniProtKB:Q6RKD8}.; ",{"$nulls":4},"p.Ala77Thr","c.229G>A","MODERATE","77/674",2,2,{"$nulls":4},"4","1192","1024","899","760","1048","891","0","0","0","0.1235",{"$nulls":20},"-0.935723","-3.96",null,"1;0.999997","-0.6",null,"0.457","0.052",{"$nulls":3},"ExAC_FIN_AF",1.515E-4,{"$nulls":7},"0/0","1184,0","0","1184","0/1","869,137","0.1362","1006",null,"chr11:64116496:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1368"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","FLRT1","chr11:64116496","FLRT1(A77T)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs770193280",1.515E-4,null,"FUNCTION: Plays a role in fibroblast growth factor-mediated signaling cascades that lead to the activation of MAP kinases. Promotes neurite outgrowth via FGFR1-mediated activation of downstream MAP kinases. Promotes an increase both in neurite number and in neurite length. May play a role in cell-cell adhesion and cell guidance via its interaction with ADGRL1/LPHN1 and ADGRL3. {ECO:0000250|UniProtKB:Q6RKD8}.; ",{"$nulls":4},"p.Ala77Thr","c.229G>A","MODERATE","77/674",2,2,{"$nulls":4},"4","1192","911","899","680","1050","796","0","0","0","0.196",{"$nulls":20},"-0.935723","-3.96",null,"1;0.999997","-0.6",null,"0.457","0.052",{"$nulls":3},"ExAC_FIN_AF",1.515E-4,{"$nulls":7},"0/0","1179,0","0","1179","0/1","696,184","0.2091","880",null,"chr11:64116496:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2147"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","GAD2","chr10:26219083","GAD2(A109A)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Catalyzes the production of GABA.; ",{"$nulls":5},"c.327G>A","HIGH",null,4,{"$nulls":5},"5","153","110","141","97","116","83","0","0","0","0.241",{"$nulls":31},"Unknown",-1,{"$nulls":4},"This gene encodes one of several forms of glutamic acid decarboxylase, identified as a major autoantigen in insulin-dependent diabetes. The enzyme encoded is responsible for catalyzing the production of gamma-aminobutyric acid from L-glutamic acid. A pathogenic role for this enzyme has been identified in the human pancreas since it has been identified as an autoantibody and an autoreactive T cell target in insulin-dependent diabetes. This gene may also play a role in the stiff man syndrome. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2008].",null,null,"0/0","152,0","0","152","0/1","80,27","0.2523","107",null,"chr10:26219083:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2887"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","GAD2","chr10:26219083","GAD2(A109A)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Catalyzes the production of GABA.; ",{"$nulls":5},"c.327G>A","HIGH",null,4,{"$nulls":5},"5","153","109","141","98","116","92","0","0","0","0.4457",{"$nulls":31},"Unknown",-1,{"$nulls":4},"This gene encodes one of several forms of glutamic acid decarboxylase, identified as a major autoantigen in insulin-dependent diabetes. The enzyme encoded is responsible for catalyzing the production of gamma-aminobutyric acid from L-glutamic acid. A pathogenic role for this enzyme has been identified in the human pancreas since it has been identified as an autoantibody and an autoreactive T cell target in insulin-dependent diabetes. This gene may also play a role in the stiff man syndrome. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2008].",null,null,"0/0","152,0","0","152","0/1","63,44","0.4112","107",null,"chr10:26219083:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4184"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","GBGT1","chr9:133153711","GBGT1(H304Y)",null,null,"topological domain (Lumenal ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens.; ",{"$nulls":4},"p.His304Tyr","c.910C>T","MODERATE","304/347",7,{"$nulls":5},"5","1102","953","818","701","955","768","0","0","0","0.1133",{"$nulls":20},"0.757522","5.65","-0.45;.","1;0.949995;0.949995;1","2.61","0.001;.","1.0","0.153;0.18",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1074,0","0","1074","0/1","829,105","0.1124","934",null,"chr9:133153711:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1155"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","GBGT1","chr9:133153711","GBGT1(H304Y)",null,null,"topological domain (Lumenal ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens.; ",{"$nulls":4},"p.His304Tyr","c.910C>T","MODERATE","304/347",7,{"$nulls":5},"4","1102","1107","818","806","956","948","0","0","0","0.1234",{"$nulls":20},"0.757522","5.65","-0.45;.","1;0.949995;0.949995;1","2.61","0.001;.","1.0","0.153;0.18",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1074,0","0","1074","0/1","919,128","0.1223","1047",null,"chr9:133153711:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1179"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","GJC2","chr1:228158254","GJC2(G166S)",null,null,"topological domain (Cytoplasmic ), compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense","rs997544625",-1,"DISEASE: Spastic paraplegia 44, autosomal recessive (SPG44) [MIM:613206]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269|PubMed:19056803}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Lymphedema, hereditary, 1C (LMPH1C) [MIM:613480]: A chronic disabling condition which results in swelling of the extremities due to altered lymphatic flow. Patients with lymphedema suffer from recurrent local infections and physical impairment. {ECO:0000269|PubMed:20537300}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: One gap junction consists of a cluster of closely packed pairs of transmembrane channels, the connexons, through which materials of low MW diffuse from one cell to a neighboring cell. May play a role in myelination in central and peripheral nervous systems. {ECO:0000269|PubMed:15192806}.; ",{"$nulls":4},"p.Gly166Ser","c.496G>A","MODERATE","166/439",2,{"$nulls":5},"5","186","191","162","165","119","124","0","0","0","0.2339",{"$nulls":20},"0.978392","-4.6","1.32","1","-0.05","0.037","0.517","0.219",{"$nulls":3},"Unknown",-1,"AD/AR","Lymphedema, hereditary, IC; Spastic paraplegia 44, autosomal recessive; Leukodystrophy, hypomyelinating, 2","Cardiovascular; Dermatologic; Neurologic",{"$nulls":3},"C2750784| C1837355| C4747646","0/0","182,0","0","182","0/1","149,32","0.1768","181",null,"chr1:228158254:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1697"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","GJC2","chr1:228158254","GJC2(G166S)",null,null,"topological domain (Cytoplasmic ), compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense","rs997544625",-1,"DISEASE: Spastic paraplegia 44, autosomal recessive (SPG44) [MIM:613206]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269|PubMed:19056803}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Lymphedema, hereditary, 1C (LMPH1C) [MIM:613480]: A chronic disabling condition which results in swelling of the extremities due to altered lymphatic flow. Patients with lymphedema suffer from recurrent local infections and physical impairment. {ECO:0000269|PubMed:20537300}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: One gap junction consists of a cluster of closely packed pairs of transmembrane channels, the connexons, through which materials of low MW diffuse from one cell to a neighboring cell. May play a role in myelination in central and peripheral nervous systems. {ECO:0000269|PubMed:15192806}.; ",{"$nulls":4},"p.Gly166Ser","c.496G>A","MODERATE","166/439",2,{"$nulls":5},"5","186","174","162","150","118","126","0","0","0","0.1587",{"$nulls":20},"0.978392","-4.6","1.32","1","-0.05","0.037","0.517","0.219",{"$nulls":3},"Unknown",-1,"AD/AR","Lymphedema, hereditary, IC; Spastic paraplegia 44, autosomal recessive; Leukodystrophy, hypomyelinating, 2","Cardiovascular; Dermatologic; Neurologic",{"$nulls":3},"C2750784| C1837355| C4747646","0/0","183,0","0","183","0/1","144,27","0.1579","171",null,"chr1:228158254:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1533"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","HEY2","chr6:125754472","HEY2(A85V)",null,null,"domain (bHLH ), region of interest (Transcriptional repression and interaction with NCOR1 and SIN3A )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Downstream effector of Notch signaling which may be required for cardiovascular development. Transcriptional repressor which binds preferentially to the canonical E box sequence 5'- CACGTG-3'. Represses transcription by the cardiac transcriptional activators GATA4 and GATA6. {ECO:0000269|PubMed:10692439, ECO:0000269|PubMed:11095750, ECO:0000269|PubMed:15485867, ECO:0000269|PubMed:16293227}.; ",{"$nulls":4},"p.Ala85Val","c.254C>T","MODERATE","85/337",4,{"$nulls":5},"5","258","282","200","212","104","123","0","0","0","0.3008",{"$nulls":20},"4.215999","-4.62",".;0.895","1","-3.36",".;0.563","0.002","0.759;0.828",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","249,0","0","249","0/1","228,43","0.1587","271",null,"chr6:125754472:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1462"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","HOXD10","chr2:176117441","HOXD10(E203G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Vertical talus, congenital (CVT) [MIM:192950]: A rare malformation characterized by vertical orientation of the talus with a rigid dorsal dislocation of the navicular, equinus deformity of the calcaneus, abduction deformity of the forefoot, and contracture of the soft tissues of the hind- and mid-foot. This condition is usually associated with multiple other congenital deformities and only rarely is an isolated deformity with familial occurrence. {ECO:0000269|PubMed:15146389}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.; ",{"$nulls":4},"p.Glu203Gly","c.608A>G","MODERATE","203/340",1,{"$nulls":5},"5","495","414","401","327","423","347","0","0","0","0.245",{"$nulls":20},"2.983136","-3.36","2.67","0.999132","-2.92","0.002","0.043","0.42",{"$nulls":3},"Unknown",-1,"AD","Vertical talus, congenital","Musculoskeletal",null,"This gene is a member of the Abd-B homeobox family and encodes a protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox D genes located on chromosome 2. The encoded nuclear protein functions as a sequence-specific transcription factor that is expressed in the developing limb buds and is involved in differentiation and limb development. Mutations in this gene have been associated with Wilm's tumor and congenital vertical talus (also known as 'rocker-bottom foot' deformity or congenital convex pes valgus) and/or a foot deformity resembling that seen in Charcot-Marie-Tooth disease. [provided by RefSeq, Jul 2008].  ",null,"C0240912","0/0","496,0","0","496","0/1","308,98","0.2414","406",null,"chr2:176117441:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2446"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","HOXD10","chr2:176117441","HOXD10(E203G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Vertical talus, congenital (CVT) [MIM:192950]: A rare malformation characterized by vertical orientation of the talus with a rigid dorsal dislocation of the navicular, equinus deformity of the calcaneus, abduction deformity of the forefoot, and contracture of the soft tissues of the hind- and mid-foot. This condition is usually associated with multiple other congenital deformities and only rarely is an isolated deformity with familial occurrence. {ECO:0000269|PubMed:15146389}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.; ",{"$nulls":4},"p.Glu203Gly","c.608A>G","MODERATE","203/340",1,{"$nulls":5},"5","495","324","401","243","424","274","0","0","0","0.3431",{"$nulls":20},"2.983136","-3.36","2.67","0.999132","-2.92","0.002","0.043","0.42",{"$nulls":3},"Unknown",-1,"AD","Vertical talus, congenital","Musculoskeletal",null,"This gene is a member of the Abd-B homeobox family and encodes a protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox D genes located on chromosome 2. The encoded nuclear protein functions as a sequence-specific transcription factor that is expressed in the developing limb buds and is involved in differentiation and limb development. Mutations in this gene have been associated with Wilm's tumor and congenital vertical talus (also known as 'rocker-bottom foot' deformity or congenital convex pes valgus) and/or a foot deformity resembling that seen in Charcot-Marie-Tooth disease. [provided by RefSeq, Jul 2008].  ",null,"C0240912","0/0","496,0","0","496","0/1","210,105","0.3333","315",null,"chr2:176117441:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.321"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","HSPA4L","chr4:127827381","HSPA4L(K708R)",{"$nulls":6},255,"PASS","Missense","rs1201851138",-1,null,"FUNCTION: Possesses chaperone activity in vitro where it inhibits aggregation of citrate synthase. {ECO:0000250}.; ",{"$nulls":4},"p.Lys708Arg","c.2123A>G","MODERATE","708/839",17,{"$nulls":5},"4","126","78","84","49",null,null,"0","0",{"$nulls":22},"3.182879","2.55","1.04;1.04;.","0.999868","-0.47","0.997;0.997;0.67","0.672;0.672;0.675","0.392;0.392;0.397",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","125,0","0","125","0/1","72,4","0.0526","76",null,"chr4:127827381:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0816"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","IL1RAPL1","chrX:29955726","IL1RAPL1(S666L)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel (PubMed:12783849). May activate the MAP kinase JNK (PubMed:15123616). Plays a role in neurite outgrowth (By similarity). During dendritic spine formation can bidirectionally induce pre- and post-synaptic differentiation of neurons by trans- synaptically binding to PTPRD (By similarity). {ECO:0000250|UniProtKB:P59823, ECO:0000250|UniProtKB:P59824, ECO:0000269|PubMed:12783849, ECO:0000269|PubMed:15123616}.; ",{"$nulls":4},"p.Ser666Leu","c.1997C>T","MODERATE","666/696",11,1,{"$nulls":4},"5","286","144","205","114","261","137","0","0","0","0.1022",{"$nulls":20},"1.922077","3.75;.","1.355;.","0.723348","-0.51;.","0.012;.","0.016;.","0.147;.",{"$nulls":3},"Unknown",-1,"XL","Mental retardation, X-linked 21/34","Neurologic",{"$nulls":3},"C0796227","0/0","285,0","0","285","0/1","132,14","0.0959","146",null,"chrX:29955726:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0702"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","IL1RAPL1","chrX:29955726","IL1RAPL1(S666L)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel (PubMed:12783849). May activate the MAP kinase JNK (PubMed:15123616). Plays a role in neurite outgrowth (By similarity). During dendritic spine formation can bidirectionally induce pre- and post-synaptic differentiation of neurons by trans- synaptically binding to PTPRD (By similarity). {ECO:0000250|UniProtKB:P59823, ECO:0000250|UniProtKB:P59824, ECO:0000269|PubMed:12783849, ECO:0000269|PubMed:15123616}.; ",{"$nulls":4},"p.Ser666Leu","c.1997C>T","MODERATE","666/696",11,1,{"$nulls":4},"5","286","187","205","124","261","162","0","0","0","0.2716",{"$nulls":20},"1.922077","3.75;.","1.355;.","0.723348","-0.51;.","0.012;.","0.016;.","0.147;.",{"$nulls":3},"Unknown",-1,"XL","Mental retardation, X-linked 21/34","Neurologic",{"$nulls":3},"C0796227","0/0","285,0","0","285","0/1","131,53","0.288","184",null,"chrX:29955726:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3387"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","IL9","chr5:135895711","IL9(N35fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Supports IL-2 independent and IL-4 independent growth of helper T-cells.; ","level2",{"$nulls":3},"p.Asn35fs","c.105delC","HIGH","35/144",1,{"$nulls":5},"5","458","395","355","311","407","342","0","0","0","0.0702",{"$nulls":5},"(IL9|ENSG00000145839|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"kJAK_STAT",{"$nulls":3},"0/0","449,0","0","449","0/1","354,28","0.0733","382",null,"chr5:135895711:TG:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0772"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","IQUB","chr7:123452748","IQUB(H791Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play roles in cilia formation and/or maintenance. {ECO:0000250}.; ",{"$nulls":4},"p.His791Tyr","c.2371C>T","MODERATE","791/791",13,{"$nulls":5},"5","214","182","178","156","168","139","0","0","0","0.3022",{"$nulls":20},"0.31863","1.9","0","1","-0.51","0.022","0.0","0.113;0.111",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","213,0","0","213","0/1","134,48","0.2637","182",null,"chr7:123452748:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2821"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","IQUB","chr7:123452748","IQUB(H791Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play roles in cilia formation and/or maintenance. {ECO:0000250}.; ",{"$nulls":4},"p.His791Tyr","c.2371C>T","MODERATE","791/791",13,{"$nulls":5},"5","214","195","178","168","168","148","0","0","0","0.3378",{"$nulls":20},"0.31863","1.9","0","1","-0.51","0.022","0.0","0.113;0.111",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","213,0","0","213","0/1","131,62","0.3212","193",null,"chr7:123452748:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2976"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","KDSR","chr18:63331874","KDSR(I303V)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense","rs1440178339",-1,"DISEASE: Erythrokeratodermia variabilis et progressiva 4 (EKVP4) [MIM:617526]: A form of erythrokeratodermia variabilis et progressiva, a genodermatosis characterized by the coexistence of two independent skin lesions: transient erythema and hyperkeratosis that is usually localized but occasionally occurs in its generalized form. Clinical presentation varies significantly within a family and from one family to another. Palmoplantar keratoderma is present in around 50% of cases. {ECO:0000269|PubMed:28575652}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS). {ECO:0000269|PubMed:28575652}.; ",{"$nulls":4},"p.Ile303Val","c.907A>G","MODERATE","303/332",10,{"$nulls":5},"5","342","307","237","206","314","280","0","0","0","0.1",{"$nulls":20},"1.814067",".;-2.11;.;-0.8","0.47;0.47;.;.","0.999894;0.998882",".;-0.42;.;-0.29","0.006;0.006;.;.",".;0.35;.;0.312",".;0.142;.;0.16",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene catalyzes the reduction of 3-ketodihydrosphingosine to dihydrosphingosine. The putative active site residues of the encoded protein are found on the cytosolic side of the endoplasmic reticulum membrane. A chromosomal rearrangement involving this gene is a cause of follicular lymphoma, also known as type II chronic lymphatic leukemia. The mutation of a conserved residue in the bovine ortholog causes spinal muscular atrophy. [provided by RefSeq, Jul 2008].  ",null,"C4479620","0/0","333,0","0","333","0/1","266,32","0.1074","298",null,"chr18:63331874:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1117"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","KSR1","chr17:27577556","KSR1(T69M)",null,null,"region of interest (Mediates association with membranes ), splice variant (In isoform 3 and isoform 4. ), helix ",{"$nulls":3},255,"PASS","Missense","rs761371576",2.269e-05,null,"FUNCTION: Scaffolding protein that is part of a multiprotein signaling complex. Promotes phosphorylation of Raf family members and activation of downstream MAP kinases. Promotes activation of MAPK1 and/or MAPK3, both in response to EGF and to cAMP. Does not have kinase activity by itself. {ECO:0000250|UniProtKB:Q61097}.; ",{"$nulls":4},"p.Thr69Met","c.206C>T","MODERATE","69/846",4,{"$nulls":5},"5","336","285","237","199","285","248","0","0","0","0.0766",{"$nulls":20},"2.166255",".;0.63;.;.;7.17;.",null,"0.894201",".;.;.;.;-1.56;.",null,".;.;.;.;0.17;.",".;.;.;.;0.341;.",{"$nulls":3},"ExAC_NFE_AF",2.269e-05,{"$nulls":7},"0/0","331,0","0","331","0/1","257,24","0.0854","281",null,"chr17:27577556:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0955"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","LDHAL6B","chr15:59207176","LDHAL6B(S79L)",{"$nulls":6},255,"PASS","Missense","rs146343279",2.2820629849383843E-4,null,null,"mitocarta",{"$nulls":3},"p.Ser79Leu","c.236C>T","MODERATE","79/381",1,1,{"$nulls":4},"5","905","662","698","472","813","528","0","0","0","0.161",{"$nulls":20},"0.569631","-2.35","0.86","0.999996;1","-2.32","0.657","0.04","0.058",{"$nulls":3},"ESP6500_AA_AF",2.2820629849383843E-4,{"$nulls":7},"0/0","902,0","0","902","0/1","548,102","0.1569","650",null,"chr15:59207176:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1568"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","LDHAL6B","chr15:59207176","LDHAL6B(S79L)",{"$nulls":6},255,"PASS","Missense","rs146343279",2.2820629849383843E-4,null,null,"mitocarta",{"$nulls":3},"p.Ser79Leu","c.236C>T","MODERATE","79/381",1,1,{"$nulls":4},"5","905","583","698","438","811","443","0","0","0","0.1896",{"$nulls":20},"0.569631","-2.35","0.86","0.999996;1","-2.32","0.657","0.04","0.058",{"$nulls":3},"ESP6500_AA_AF",2.2820629849383843E-4,{"$nulls":7},"0/0","902,0","0","902","0/1","461,106","0.1869","567",null,"chr15:59207176:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1986"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","LNP1","chr3:100429845","LNP1(L39R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving LNP1 is found in a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(3;11)(q12.2;p15.4) with NUP98. {ECO:0000269|PubMed:16467868}.; ",{"$nulls":5},"p.Leu39Arg","c.116T>G","MODERATE","39/191",2,{"$nulls":5},"5","255","193","175","133","220","168","0","0","0","0.1488",{"$nulls":20},"0.493845",null,"0.345;.","1","0.93","0.039;.","0.159;0.152","0.115;0.127",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","253,0","0","253","0/1","160,28","0.1489","188",null,"chr3:100429845:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1278"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","LRCH2","chrX:115123178","LRCH2(S622A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser622Ala","c.1864T>G","MODERATE","622/765",18,{"$nulls":5},"5","614","273","402","170","569","250","0","0","0","0.108",{"$nulls":20},"1.931155","5.64;5.59","1.345;.","0.932114","-0.78","0.0;.","0.217;0.136","0.108;0.121",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","594,0","0","594","0/1","212,34","0.1382","246",null,"chrX:115123178:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1235"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","LRWD1","chr7:102468318","LRWD1(Q289fs)",null,null,"repeat (WD 1 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Required for G1/S transition. Recruits and stabilizes the origin recognition complex (ORC) onto chromatin during G1 to establish pre-replication complex (preRC) and to heterochromatic sites in post-replicated cells. Binds a combination of DNA and histone methylation repressive marks on heterochromatin. Binds histone H3 and H4 trimethylation marks H3K9me3, H3K27me3 and H4K20me3 in a cooperative manner with DNA methylation. Required for silencing of major satellite repeats. May be important ORC2, ORC3 and ORC4 stability. {ECO:0000269|PubMed:20850016, ECO:0000269|PubMed:20932478, ECO:0000269|PubMed:21029866, ECO:0000269|PubMed:22427655, ECO:0000269|PubMed:22645314}.; ",{"$nulls":4},"p.Gln289fs","c.865dupC","HIGH","289/647",7,{"$nulls":5},"4",null,null,"173","117","191","136",null,null,"0","0.0588",{"$nulls":5},"(LRWD1|ENSG00000161036|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","213,0","0","213","0/1","133,13","0.089","146",null,"chr7:102468318:G:GC",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0769"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","MDGA1","chr6:37650354","MDGA1(E455fs)",null,null,"domain (Ig-like 5 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Required for radial migration of cortical neurons in the superficial layer of the neocortex (By similarity). Plays a role in the formation or maintenance of inhibitory synapses. May function by inhibiting the activity of NLGN2. {ECO:0000250, ECO:0000269|PubMed:23248271}.; ",{"$nulls":4},"p.Glu455fs","c.1362_1363delCG","HIGH","454/973",8,{"$nulls":5},"5","243","210","163","145","184","164","0.0048","0.0048","0","0.2561",{"$nulls":5},"(MDGA1|ENSG00000112139|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","208,1","0.0048","209","0/1","128,51","0.2849","179",null,"chr6:37650354:TCG:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2483"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","MDGA1","chr6:37650354","MDGA1(E455fs)",null,null,"domain (Ig-like 5 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Required for radial migration of cortical neurons in the superficial layer of the neocortex (By similarity). Plays a role in the formation or maintenance of inhibitory synapses. May function by inhibiting the activity of NLGN2. {ECO:0000250, ECO:0000269|PubMed:23248271}.; ",{"$nulls":4},"p.Glu455fs","c.1362_1363delCG","HIGH","454/973",8,{"$nulls":5},"5","243","197","163","143","185","160","0.0048","0.0048","0","0.2687",{"$nulls":5},"(MDGA1|ENSG00000112139|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","208,1","0.0048","209","0/1","113,51","0.311","164",null,"chr6:37650354:TCG:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2448"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","MED12L","chr3:151411316","MED12L(M1948I)",null,null,"compositionally biased region (Gln-rich ), splice variant (In isoform 2 and isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met1948Ile","c.5844G>A","MODERATE","1948/2145",39,{"$nulls":5},"5","700","766","529","574","601","616","0","0","0","0.0682",{"$nulls":20},"2.218051","0.4","1.32","0.931938;1","-1.35","0.033","0.336","0.423",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN280885","0/0","690,0","0","690","0/1","695,51","0.0684","746",null,"chr3:151411316:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0645"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","MED12L","chr3:151411316","MED12L(M1948I)",null,null,"compositionally biased region (Gln-rich ), splice variant (In isoform 2 and isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Met1948Ile","c.5844G>A","MODERATE","1948/2145",39,{"$nulls":5},"5","700","803","529","603","600","675","0","0","0","0.1096",{"$nulls":20},"2.218051","0.4","1.32","0.931938;1","-1.35","0.033","0.336","0.423",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN280885","0/0","685,0","0","685","0/1","688,90","0.1157","778",null,"chr3:151411316:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1177"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","MED13L","chr12:115982380","MED13L(F1722fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=A chromosomal aberration involving MED13L is found in a patient with transposition of the great arteries, dextro- looped and mental retardation. Translocation t(12;17)(q24.1;q21). {ECO:0000269|PubMed:14638541}.; DISEASE: Mental retardation and distinctive facial features with or without cardiac defects (MRFACD) [MIM:616789]: An autosomal dominant, syndromic form of mental retardation characterized by delayed psychomotor development, profound language impairment, and facial dysmorphism, including frontal bossing, upslanting palpebral fissures, depressed nasal bridge with bulbous tip, and macrostomia. There is variable penetrance of cardiac malformations, ranging from no malformations to patent foramen ovale to septal defects and/or transposition of the great arteries. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:24781760, ECO:0000269|PubMed:25167861, ECO:0000269|PubMed:25356899, ECO:0000269|PubMed:25712080, ECO:0000269|PubMed:25758992}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. This subunit may specifically regulate transcription of targets of the Wnt signaling pathway and SHH signaling pathway.; ",{"$nulls":4},"p.Phe1722fs","c.5165_5175+3delTCATTCTCCAGGTT","HIGH","1722/2210",22,{"$nulls":5},"3",null,null,"168","150",{"$nulls":11},"(MED13L|ENSG00000123066|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Transposition of the great arteries, dextro-looped 1; Congenital heart defects and intellectual disability; Intellectual disability, autosomal recessive","Cardiovascular; Craniofacial; Neurologic",{"$nulls":3},"C4225208| C1837341","0/0","224,0","0","224","0/1","181,11","0.0573","192",null,"chr12:115982380:TAACCTGGAGAATGA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0733"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","MIOS","chr7:7605959","MIOS(V809fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210). {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.; ",{"$nulls":4},"p.Val809fs","c.2424delA","HIGH","808/875",12,{"$nulls":5},"5","414","406","328","302","378","382","0","0","0","0.144",{"$nulls":5},"(MIOS|ENSG00000164654|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","397,0","0","397","0/1","314,64","0.1693","378",null,"chr7:7605959:GA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.149"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","MIOS","chr7:7605959","MIOS(V809fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210). {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.; ",{"$nulls":4},"p.Val809fs","c.2424delA","HIGH","808/875",12,{"$nulls":5},"5","414","384","328","281","379","368","0","0","0","0.1739",{"$nulls":5},"(MIOS|ENSG00000164654|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","397,0","0","397","0/1","295,67","0.1851","362",null,"chr7:7605959:GA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1815"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","MKI67","chr10:128108956","MKI67(S962P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable). {ECO:0000250|UniProtKB:E9PVX6, ECO:0000269|PubMed:10878551, ECO:0000269|PubMed:24867636, ECO:0000269|PubMed:27362226}.; ",{"$nulls":4},"p.Ser962Pro","c.2884T>C","MODERATE","962/3256",13,{"$nulls":5},"5","842","756","655","548","774","692","0","0","0","0.1084",{"$nulls":20},"0.809558","4.99;5.03",".;0.345","1","-1.32","0.952;0.92","0.232;0.235","0.169;0.144",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","837,0","0","837","0/1","664,85","0.1135","749",null,"chr10:128108956:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1058"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","MTO1","chr6:73497736","MTO1(A626V)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U34) of the wobble uridine base in mitochondrial tRNAs. {ECO:0000269|PubMed:12011058}.; ","mitocarta",{"$nulls":3},"p.Ala626Val","c.1877C>T","MODERATE","626/732",12,{"$nulls":5},"5","273","232","235","199","206","192","0","0","0","0.0938",{"$nulls":20},"4.710101",null,".;.;.;2.165","0.999992;0.999992;0.999976;0.999992","-3.67","0.999;0.998;.;0.999","0.017;0.018;0.021;0.021","0.318;0.389;0.396;0.367",{"$nulls":3},"Unknown",-1,"AR","Combined oxidative phosphorylation deficiency 10","Biochemical; Cardiovascular; Neurologic",{"$nulls":3},"C3553529","0/0","272,0","0","272","0/1","207,22","0.0961","229",null,"chr6:73497736:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0955"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","MTO1","chr6:73497736","MTO1(A626V)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U34) of the wobble uridine base in mitochondrial tRNAs. {ECO:0000269|PubMed:12011058}.; ","mitocarta",{"$nulls":3},"p.Ala626Val","c.1877C>T","MODERATE","626/732",12,{"$nulls":5},"5","273","348","235","282","205","275","0","0","0","0.0691",{"$nulls":20},"4.710101",null,".;.;.;2.165","0.999992;0.999992;0.999976;0.999992","-3.67","0.999;0.998;.;0.999","0.017;0.018;0.021;0.021","0.318;0.389;0.396;0.367",{"$nulls":3},"Unknown",-1,"AR","Combined oxidative phosphorylation deficiency 10","Biochemical; Cardiovascular; Neurologic",{"$nulls":3},"C3553529","0/0","271,0","0","271","0/1","314,24","0.071","338",null,"chr6:73497736:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0709"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","MYOM3","chr1:24084525","MYOM3(F611fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May link the intermediate filament cytoskeleton to the M-disk of the myofibrils in striated muscle. {ECO:0000250}.; ",{"$nulls":4},"p.Phe611fs","c.1830_1912delTTTCAGAGACACACAGACCTCTGTCTCCCTGACATGGGATCCTGTGAAAGACCCAGAGCTCCTGGGTTATTACATCTACTCCC","HIGH","610/1437",16,{"$nulls":20},"24084608",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr1:24084525:CGGGAGTAGATGTAATAACCCAGGAGCTCTGGGTCTTTCACAGGATCCCATGTCAGGGAGACAGAGGTCTGTGTGTCTCTGAAA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","NADK","chr1:1757246","NADK(I214V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ile214Val","c.640A>G","MODERATE","214/591",6,{"$nulls":5},"3",null,null,"467","433","525","517",null,null,"0","0.0503",{"$nulls":20},"1.240675","1.03;1.03;0.67;1.03","1.025;1.025;.;.","0.997675;0.989553;0.989553;0.997675;0.997675","-0.8;-0.8;-0.78;-0.8","0.06;0.06;.;.","0.132;0.132;0.316;0.214","0.198;0.197;0.365;0.195",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","624,0","0","624","0/1","568,30","0.0502","598",null,"chr1:1757246:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0508"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","NDST3","chr4:118240639","NDST3(P745L)",null,null,"topological domain (Lumenal ), region of interest (Heparan sulfate N-sulfotransferase 3 ), splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs776638744",1.501E-5,null,"FUNCTION: Essential bifunctional enzyme that catalyzes both the N- deacetylation and the N-sulfation of glucosamine (GlcNAc) of the glycosaminoglycan in heparan sulfate. Modifies the GlcNAc-GlcA disaccharide repeating sugar backbone to make N-sulfated heparosan, a prerequisite substrate for later modifications in heparin biosynthesis. Has high deacetylase activity but low sulfotransferase activity. {ECO:0000269|PubMed:9915799}.; ",{"$nulls":4},"p.Pro745Leu","c.2234C>T","MODERATE","745/873",11,{"$nulls":5},"5","545","457","368","308","507","420","0","0","0","0.1381",{"$nulls":20},"3.694746","-1.47","2.86","1","-8.08","1.0","0.002","0.865",{"$nulls":3},"ExAC_NFE_AF",1.501E-5,{"$nulls":7},"0/0","535,0","0","535","0/1","378,65","0.1467","443",null,"chr4:118240639:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1396"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","NDST3","chr4:118240639","NDST3(P745L)",null,null,"topological domain (Lumenal ), region of interest (Heparan sulfate N-sulfotransferase 3 ), splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs776638744",1.501E-5,null,"FUNCTION: Essential bifunctional enzyme that catalyzes both the N- deacetylation and the N-sulfation of glucosamine (GlcNAc) of the glycosaminoglycan in heparan sulfate. Modifies the GlcNAc-GlcA disaccharide repeating sugar backbone to make N-sulfated heparosan, a prerequisite substrate for later modifications in heparin biosynthesis. Has high deacetylase activity but low sulfotransferase activity. {ECO:0000269|PubMed:9915799}.; ",{"$nulls":4},"p.Pro745Leu","c.2234C>T","MODERATE","745/873",11,{"$nulls":5},"5","545","396","368","277","508","361","0","0","0","0.1994",{"$nulls":20},"3.694746","-1.47","2.86","1","-8.08","1.0","0.002","0.865",{"$nulls":3},"ExAC_NFE_AF",1.501E-5,{"$nulls":7},"0/0","537,0","0","537","0/1","302,77","0.2032","379",null,"chr4:118240639:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1805"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","NME9","chr3:138306477","NME9(S155L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a regulator of microtubule physiology.; ",{"$nulls":4},"p.Ser155Leu","c.464C>T","MODERATE","155/330",7,1,{"$nulls":4},"4","644","724","451","484",null,null,"0","0",{"$nulls":22},"2.426412","0.83;0.83;0.87;0.86;0.88",".;.;.;2.035;.","0.999998;1;1;1;0.999998;0.999998","-2.3;-2.3;-2.42;-2.48;-2.71","0.045;0.045;0.034;0.016;.","0.16;0.16;0.021;0.187;0.026","0.191;0.183;0.198;0.145;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","634,0","0","634","0/1","670,37","0.0523","707",null,"chr3:138306477:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0517"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","NME9","chr3:138306477","NME9(S155L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a regulator of microtubule physiology.; ",{"$nulls":4},"p.Ser155Leu","c.464C>T","MODERATE","155/330",7,1,{"$nulls":4},"5","644","804","451","544","602","745","0","0","0","0.1128",{"$nulls":20},"2.426412","0.83;0.83;0.87;0.86;0.88",".;.;.;2.035;.","0.999998;1;1;1;0.999998;0.999998","-2.3;-2.3;-2.42;-2.48;-2.71","0.045;0.045;0.034;0.016;.","0.16;0.16;0.021;0.187;0.026","0.191;0.183;0.198;0.145;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","627,0","0","627","0/1","681,93","0.1202","774",null,"chr3:138306477:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.125"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","NNT","chr5:43653028","NNT(L625Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane. May play a role in reactive oxygen species (ROS) detoxification in the adrenal gland. {ECO:0000269|PubMed:22634753}.; ","mitocarta",{"$nulls":3},"p.Leu625Gln","c.1874T>A","MODERATE","625/1086",14,{"$nulls":5},"5","362","419","295","323","290","337","0","0","0","0.1187",{"$nulls":20},"4.334534","-3.21","3.855;3.855;.","1","-5.31;-5.31;-5.68","1.0;1.0;.","0.0","0.969;0.969;0.972",{"$nulls":3},"Unknown",-1,"AR","Glucocorticoid deficiency 4","Endocrine",null,"This gene encodes an integral protein of the inner mitochondrial membrane. The enzyme couples hydride transfer between NAD(H) and NADP(+) to proton translocation across the inner mitochondrial membrane. Under most physiological conditions, the enzyme uses energy from the mitochondrial proton gradient to produce high concentrations of NADPH. The resulting NADPH is used for biosynthesis and in free radical detoxification. Two alternatively spliced variants, encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008].",null,"C3553587","0/0","354,0","0","354","0/1","351,42","0.1069","393",null,"chr5:43653028:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1053"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","OAS2","chr12:113003100","OAS2(R393W)",{"$nulls":6},255,"PASS","Missense","rs759701630",1.5000000000000002E-5,null,"FUNCTION: Interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate antiviral response (PubMed:10464285, PubMed:9880569). Activated by detection of double stranded RNA (dsRNA): polymerizes higher oligomers of 2'- 5'-oligoadenylates (2-5A) from ATP which then bind to the inactive monomeric form of ribonuclease L (RNASEL) leading to its dimerization and subsequent activation (PubMed:10464285, PubMed:9880569, PubMed:11682059). Activation of RNASEL leads to degradation of cellular as well as viral RNA, resulting in the inhibition of protein synthesis, thus terminating viral replication (PubMed:10464285, PubMed:9880569). Can mediate the antiviral effect via the classical RNASEL-dependent pathway or an alternative antiviral pathway independent of RNASEL (PubMed:21142819). In addition, it may also play a role in other cellular processes such as apoptosis, cell growth, differentiation and gene regulation (PubMed:21142819). May act as a negative regulator of lactation, stopping lactation in virally infected mammary gland lobules, thereby preventing transmission of viruses to neonates (By similarity). Non-infected lobules would not be affected, allowing efficient pup feeding during infection (By similarity). {ECO:0000250|UniProtKB:E9Q9A9, ECO:0000269|PubMed:10464285, ECO:0000269|PubMed:11682059, ECO:0000269|PubMed:19923450, ECO:0000269|PubMed:9880569, ECO:0000303|PubMed:21142819}.; ",{"$nulls":4},"p.Arg393Trp","c.1177C>T","MODERATE","393/726",6,{"$nulls":5},"5","267","212","175","135","240","193","0","0","0","0.0829",{"$nulls":20},"2.626872","3.12;3.12;.","1.04;1.04;.","1","-4.7;-4.67;.","0.99;0.987;.","0.0;0.0;.","0.259;0.256;0.258",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,{"$nulls":7},"0/0","265,0","0","265","0/1","188,23","0.109","211",null,"chr12:113003100:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1259"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","OAS2","chr12:113003100","OAS2(R393W)",{"$nulls":6},255,"PASS","Missense","rs759701630",1.5000000000000002E-5,null,"FUNCTION: Interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate antiviral response (PubMed:10464285, PubMed:9880569). Activated by detection of double stranded RNA (dsRNA): polymerizes higher oligomers of 2'- 5'-oligoadenylates (2-5A) from ATP which then bind to the inactive monomeric form of ribonuclease L (RNASEL) leading to its dimerization and subsequent activation (PubMed:10464285, PubMed:9880569, PubMed:11682059). Activation of RNASEL leads to degradation of cellular as well as viral RNA, resulting in the inhibition of protein synthesis, thus terminating viral replication (PubMed:10464285, PubMed:9880569). Can mediate the antiviral effect via the classical RNASEL-dependent pathway or an alternative antiviral pathway independent of RNASEL (PubMed:21142819). In addition, it may also play a role in other cellular processes such as apoptosis, cell growth, differentiation and gene regulation (PubMed:21142819). May act as a negative regulator of lactation, stopping lactation in virally infected mammary gland lobules, thereby preventing transmission of viruses to neonates (By similarity). Non-infected lobules would not be affected, allowing efficient pup feeding during infection (By similarity). {ECO:0000250|UniProtKB:E9Q9A9, ECO:0000269|PubMed:10464285, ECO:0000269|PubMed:11682059, ECO:0000269|PubMed:19923450, ECO:0000269|PubMed:9880569, ECO:0000303|PubMed:21142819}.; ",{"$nulls":4},"p.Arg393Trp","c.1177C>T","MODERATE","393/726",6,{"$nulls":5},"5","267","299","175","195","241","277","0","0","0","0.1336",{"$nulls":20},"2.626872","3.12;3.12;.","1.04;1.04;.","1","-4.7;-4.67;.","0.99;0.987;.","0.0;0.0;.","0.259;0.256;0.258",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,{"$nulls":7},"0/0","263,0","0","263","0/1","250,41","0.1409","291",null,"chr12:113003100:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1436"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","PDGFD","chr11:103943463","PDGFD(R254Q)",{"$nulls":6},255,"PASS","Missense","rs147536650",0.000992063492063492,null,"FUNCTION: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Plays an important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By similarity). {ECO:0000250, ECO:0000269|PubMed:11331881, ECO:0000269|PubMed:15271796}.; ",{"$nulls":4},"p.Arg254Gln","c.761G>A","MODERATE","254/370",5,1,{"$nulls":4},"4","205","153",null,null,"141","110","0","0","0","0.1273",{"$nulls":20},"1.581555","1.66","2.325;.","0.989391;0.999997","-1.43;-1.26","0.913;0.948","0.002","0.288;0.245",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":7},"0/0","206,0","0","206","0/1","137,14","0.0927","151",null,"chr11:103943463:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","PDGFD","chr11:103943463","PDGFD(R254Q)",{"$nulls":6},255,"PASS","Missense","rs147536650",0.000992063492063492,null,"FUNCTION: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Plays an important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By similarity). {ECO:0000250, ECO:0000269|PubMed:11331881, ECO:0000269|PubMed:15271796}.; ",{"$nulls":4},"p.Arg254Gln","c.761G>A","MODERATE","254/370",5,1,{"$nulls":4},"5","205","156","192","149","141","117","0","0","0","0.1795",{"$nulls":20},"1.581555","1.66","2.325;.","0.989391;0.999997","-1.43;-1.26","0.913;0.948","0.002","0.288;0.245",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":7},"0/0","206,0","0","206","0/1","128,26","0.1688","154",null,"chr11:103943463:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1745"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","PDHA1","chrX:19353072","PDHA1(Splicing Acceptor/Donor Loss)",null,null,"splice variant (In isoform 3. ), helix ",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Pyruvate dehydrogenase E1-alpha deficiency (PDHAD) [MIM:312170]: An enzymatic defect causing primary lactic acidosis in children. It is associated with a broad clinical spectrum ranging from fatal lactic acidosis in the newborn to chronic neurologic dysfunction with structural abnormalities in the central nervous system without systemic acidosis. {ECO:0000269|PubMed:1293379, ECO:0000269|PubMed:1338114, ECO:0000269|PubMed:1551669, ECO:0000269|PubMed:1909401, ECO:0000269|PubMed:27864847, ECO:0000269|PubMed:7545958, ECO:0000269|PubMed:7573035, ECO:0000269|PubMed:7757088, ECO:0000269|PubMed:7887409, ECO:0000269|PubMed:7967473, ECO:0000269|PubMed:8032855, ECO:0000269|PubMed:8199595, ECO:0000269|PubMed:8498846, ECO:0000269|PubMed:8504306, ECO:0000269|PubMed:8664900, ECO:0000269|PubMed:8844217, ECO:0000269|PubMed:9266390, ECO:0000269|PubMed:9671272}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle. {ECO:0000269|PubMed:19081061, ECO:0000269|PubMed:7782287}.; ","mito100|mitocarta",{"$nulls":3},"p.Gly178_Lys180delinsGlu","c.533-9_538delCATTTCCAGGACGAA","HIGH","178/428",6,{"$nulls":5},"4",null,null,"266","167","315","197",null,null,"0","0.066",{"$nulls":31},"Unknown",-1,"XL","Pyruvate dehydrogenase E1-alpha deficiency; Leigh syndrome, X-linked","Biochemical; Neurologic",{"$nulls":3},"C1839413","0/0","388,0","0","388","0/1","225,17","0.0702","242",null,"chrX:19353072:CCATTTCCAGGACGAA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0838"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","PLEKHA5","chr12:19274630","PLEKHA5(S320R)",null,null,"splice variant (In isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser320Arg","c.960C>G","MODERATE","320/1282",11,{"$nulls":5},"5","221","183","188","162","185","162","0","0","0","0.2222",{"$nulls":20},"1.847959","2.84;2.46;2.89;2.88;2.88;2.89",".;.;1.095;1.095;.;.","0.97245;0.97245;0.97245;0.97245;0.97245;0.97245;0.97245;0.955068;0.955068;0.956234","-1.96;-1.76;-2.04;-2.04;-1.9;-1.73",".;.;0.004;0.007;.;.","0.131;0.313;0.181;0.236;0.062;0.235","0.201;0.228;0.213;0.178;0.187;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","224,0","0","224","0/1","142,45","0.2406","187",null,"chr12:19274630:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2469"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","PLEKHA5","chr12:19274630","PLEKHA5(S320R)",null,null,"splice variant (In isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser320Arg","c.960C>G","MODERATE","320/1282",11,{"$nulls":5},"5","221","150","188","128","185","129","0","0","0","0.2171",{"$nulls":20},"1.847959","2.84;2.46;2.89;2.88;2.88;2.89",".;.;1.095;1.095;.;.","0.97245;0.97245;0.97245;0.97245;0.97245;0.97245;0.97245;0.955068;0.955068;0.956234","-1.96;-1.76;-2.04;-2.04;-1.9;-1.73",".;.;0.004;0.007;.;.","0.131;0.313;0.181;0.236;0.062;0.235","0.201;0.228;0.213;0.178;0.187;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","225,0","0","225","0/1","117,33","0.22","150",null,"chr12:19274630:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2422"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","PLEKHM2","chr1:15728093","PLEKHM2(H592R)",{"$nulls":6},255,"PASS","Missense","rs1039237522",-1,null,"FUNCTION: May play a role in the regulation of conventional kinesin activity. Required for maintenance of the Golgi apparatus organization. May play a role in membrane tubulation (PubMed:15905402). May play a role in lysosomes movement and localization at the cell periphery (PubMed:25898167). {ECO:0000269|PubMed:15905402, ECO:0000269|PubMed:25898167}.; ",{"$nulls":4},"p.His592Arg","c.1775A>G","MODERATE","592/1019",10,{"$nulls":5},"5","480","413","468","395","350","318","0","0","0","0.1352",{"$nulls":20},"3.836888","0.89;0.87;.","1.525;.;.","0.999999","-2.13;-2.13;.","0.993;.;.","0.019;0.019;.","0.683;0.581;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","484,0","0","484","0/1","359,52","0.1265","411",null,"chr1:15728093:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1215"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","POU5F1B","chr8:127416264","POU5F1B(P133L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Shows weak transcriptional activator activity. {ECO:0000269|PubMed:18949397}.; ",{"$nulls":4},"p.Pro133Leu","c.398C>T","MODERATE","133/359",2,{"$nulls":5},"4","352","855","267","646","322","772","0","0","0","0.0855",{"$nulls":20},"0.343027",".;1.95","2.085","0.999789",".;-1.53","0.348",".;0.189",".;0.051",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","351,0","0","351","0/1","758,90","0.1061","848",null,"chr8:127416264:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1006"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","POU5F1B","chr8:127416264","POU5F1B(P133L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Shows weak transcriptional activator activity. {ECO:0000269|PubMed:18949397}.; ",{"$nulls":4},"p.Pro133Leu","c.398C>T","MODERATE","133/359",2,{"$nulls":5},"4","352","913","267","684","322","822","0","0","0","0.0985",{"$nulls":20},"0.343027",".;1.95","2.085","0.999789",".;-1.53","0.348",".;0.189",".;0.051",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","352,0","0","352","0/1","798,94","0.1054","892",null,"chr8:127416264:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1096"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","PROX2","chr14:74862873","PROX2(T321N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription regulator. Does not seem to be essential for embryonic development and postnatal survival (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Thr321Asn","c.962C>A","MODERATE","321/592",1,{"$nulls":5},"5","698","600","540","470","611","530","0","0","0","0.1358",{"$nulls":20},"0.355941","0.99",null,"1","-0.52","0.504","0.086","0.076",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","671,0","0","671","0/1","510,76","0.1297","586",null,"chr14:74862873:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1277"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","PROX2","chr14:74862873","PROX2(T321N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription regulator. Does not seem to be essential for embryonic development and postnatal survival (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Thr321Asn","c.962C>A","MODERATE","321/592",1,{"$nulls":5},"5","698","646","540","501","612","581","0","0","0","0.2151",{"$nulls":20},"0.355941","0.99",null,"1","-0.52","0.504","0.086","0.076",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","672,0","0","672","0/1","482,136","0.2201","618",null,"chr14:74862873:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2196"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","PTPRN2","chr7:157898687","PTPRN2(T592A)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs1440243662",-1,"DISEASE: Note=Autoantigen in insulin-dependent diabetes mellitus (IDDM). {ECO:0000269|PubMed:8637868, ECO:0000269|PubMed:8798755, ECO:0000269|PubMed:8878534}.; ","FUNCTION: Plays a role in vesicle-mediated secretory processes. Required for normal accumulation of secretory vesicles in hippocampus, pituitary and pancreatic islets. Required for the accumulation of normal levels of insulin-containing vesicles and preventing their degradation. Plays a role in insulin secretion in response to glucose stimuli. Required for normal accumulation of the neurotransmitters norepinephrine, dopamine and serotonin in the brain. In females, but not in males, required for normal accumulation and secretion of pituitary hormones, such as luteinizing hormone (LH) and follicle-stimulating hormone (FSH) (By similarity). Required to maintain normal levels of renin expression and renin release (By similarity). May regulate catalytic active protein-tyrosine phosphatases such as PTPRA through dimerization (By similarity). Has phosphatidylinositol phosphatase activity; the PIPase activity is involved in its ability to regulate insulin secretion. Can dephosphorylate phosphatidylinositol 4,5-biphosphate (PI(4,5)P2), phosphatidylinositol 5-phosphate and phosphatidylinositol 3- phosphate (By similarity). Regulates PI(4,5)P2 level in the plasma membrane and localization of cofilin at the plasma membrane and thus is indirectly involved in regulation of actin dynamics related to cell migration and metastasis; upon hydrolyzation of PI(4,5)P2 cofilin is released from the plasma membrane and acts in the cytoplasm in severing F-actin filaments (PubMed:26620550). {ECO:0000250|UniProtKB:P80560, ECO:0000250|UniProtKB:Q63475, ECO:0000269|PubMed:26620550}.; ",{"$nulls":5},"c.1774A>G","HIGH",null,12,{"$nulls":5},"5","232","214","180","158","201","184","0","0","0","0.1793",{"$nulls":20},"0.343096","4.19;4.16;4.15;4.15",".;.;.;0.49","1","-1.24;-1.63;-1.63;-1.64","0.028;0.035;.;0.035","0.611;0.583;0.732;0.704","0.151;0.129;0.137;0.164",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","231,0","0","231","0/1","170,37","0.1787","207",null,"chr7:157898687:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1709"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","PUS7","chr7:105468379","PUS7(DY494EN)",null,null,"domain (TRUD ), sequence variant (In IDDABS. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Pseudouridylate synthase that catalyzes pseudouridylation of RNAs (PubMed:28073919, PubMed:29628141). Acts as a regulator of protein synthesis in embryonic stem cells by mediating pseudouridylation of RNA fragments derived from tRNAs (tRFs): pseudouridylated tRFs inhibit translation by targeting the translation initiation complex (PubMed:29628141). Also catalyzes pseudouridylation of mRNAs: mediates pseudouridylation of mRNAs with the consensus sequence 5'-UGUAG-3' (PubMed:28073919). In addition to mRNAs and tRNAs, binds other types of RNAs, such as snRNAs, Y RNAs and vault RNAs, suggesting that it can catalyze pseudouridylation of many RNA types (PubMed:29628141). {ECO:0000269|PubMed:28073919, ECO:0000269|PubMed:29628141}.; ",{"$nulls":4},"p.AspTyr494GluAsn","c.1482_1483delCTinsGA","MODERATE","494/661",12,{"$nulls":5},"4","643","603","440","410","557","528","0","0","0","0.1553",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C5193039","0/0","622,0","0","622","0/1","453,98","0.1779","551",null,"chr7:105468379:AG:TC",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1659"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","RASGRP4","chr19:38415081","RASGRP4(N332del)",{"$nulls":6},255,"PASS","Inframe Indel","rs1307704677",-1,null,"FUNCTION: Functions as a cation- and diacylglycerol (DAG)- regulated nucleotide exchange factor activating Ras through the exchange of bound GDP for GTP. May function in mast cells differentiation. {ECO:0000269|PubMed:11880369, ECO:0000269|PubMed:11956218, ECO:0000269|PubMed:12493770, ECO:0000269|PubMed:18024961}.; ","level2",{"$nulls":3},"p.Asn332del","c.994_996delAAC","MODERATE","332/673",9,{"$nulls":5},"4","658","614","490","439","535","508","0","0","0","0.1535",{"$nulls":31},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","594,0","0","594","0/1","449,86","0.1607","535",null,"chr19:38415081:AGTT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1526"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","RAX","chr18:59269086","RAX(P320Q)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs199988037",6.838e-05,null,"FUNCTION: Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE-1/Ret 1) in the photoreceptor cell-specific arrestin promoter.; ",{"$nulls":4},"p.Pro320Gln","c.959C>A","MODERATE","320/346",3,{"$nulls":5},"5","641","444","448","301","573","391","0","0","0","0.0512",{"$nulls":20},"3.6109210000000003","-3.31","1.285","1","-3.18","1.0","0.336","0.165",{"$nulls":3},"ExAC_NFE_AF",6.838e-05,"AR","Microphthalmia, isolated 3","Ophthalmologic",{"$nulls":3},"CN120488| C1970237","0/0","626,0","0","626","0/1","399,29","0.0678","428",null,"chr18:59269086:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0598"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","RBM22","chr5:150696692","RBM22(D129G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the first step of pre-mRNA splicing. Binds directly to the internal stem-loop (ISL) domain of the U6 snRNA and to the pre-mRNA intron near the 5' splice site during the activation and catalytic phases of the spliceosome cycle. Involved in both translocations of the nuclear SLU7 to the cytoplasm and the cytosolic calcium-binding protein PDCD6 to the nucleus upon cellular stress responses. {ECO:0000269|PubMed:17045351, ECO:0000269|PubMed:21122810, ECO:0000269|PubMed:22246180}.; ",{"$nulls":4},"p.Asp129Gly","c.386A>G","MODERATE","129/420",6,{"$nulls":5},"5","517","413","397","302","445","376","0","0","0","0.1489",{"$nulls":20},"3.437137","2.46","1.92;.;.","1","-4.31;-4.62;-3.76","0.05;.;.","0.059;0.025;0.075","0.629;0.717;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes an RNA binding protein. The encoded protein may play a role in cell division and may be involved in pre-mRNA splicing. Related pseudogenes exist on chromosomes 6, 7, 9, 13, 16, 18, and X. [provided by RefSeq, Mar 2009].  ",null,null,"0/0","516,0","0","516","0/1","337,61","0.1533","398",null,"chr5:150696692:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1523"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","RCN2","chr15:76931978","RCN2(V47fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Not known. Binds calcium.; ",{"$nulls":4},"p.Val47fs","c.138_142delCGTCC","HIGH","46/335",1,{"$nulls":5},"3","36","15",{"$nulls":4},"0","0",{"$nulls":7},"(RCN2|ENSG00000117906|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","38,0","0","38","0/1","12,3","0.2","15",null,"chr15:76931978:GCGTCC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","RMI1","chr9:84001099","RMI1(N38fs)",null,null,"helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Promotes TOP3A binding to double Holliday junctions (DHJ) and hence stimulates TOP3A-mediated dissolution. Required for BLM phosphorylation during mitosis. Within the BLM complex, required for BLM and TOP3A stability. {ECO:0000269|PubMed:15775963, ECO:0000269|PubMed:16537486, ECO:0000269|PubMed:16595695}.; ",{"$nulls":4},"p.Asn38fs","c.114delT","HIGH","38/625",3,{"$nulls":5},"4",null,null,"302","308","301","301",null,null,"0","0.1262",{"$nulls":5},"(RMI1|ENSG00000178966|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","325,38","0.1047","363",null,"chr9:84001099:AT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1136"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","RNF31","chr14:24150399","RNF31(S383T)",null,null,"region of interest (Polyubiquitin-binding ), modified residue (Phosphoserine), splice variant (In isoform 2. )","modified-residue:Phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase component of the LUBAC complex which conjugates linear ('Met-1'-linked) polyubiquitin chains to substrates and plays a key role in NF-kappa-B activation and regulation of inflammation (PubMed:17006537, PubMed:19136968, PubMed:20005846, PubMed:21455173, PubMed:21455180, PubMed:21455181, PubMed:22863777, PubMed:28189684). LUBAC conjugates linear polyubiquitin to IKBKG and RIPK1 and is involved in activation of the canonical NF-kappa-B and the JNK signaling pathways (PubMed:17006537, PubMed:19136968, PubMed:20005846, PubMed:21455173, PubMed:21455180, PubMed:21455181, PubMed:22863777, PubMed:28189684). Linear ubiquitination mediated by the LUBAC complex interferes with TNF-induced cell death and thereby prevents inflammation (PubMed:21455173, PubMed:28189684). LUBAC is recruited to the TNF-R1 signaling complex (TNF-RSC) following polyubiquitination of TNF-RSC components by BIRC2 and/or BIRC3 and to conjugate linear polyubiquitin to IKBKG and possibly other components contributing to the stability of the complex (PubMed:20005846, PubMed:27458237). Together with OTULIN, the LUBAC complex regulates the canonical Wnt signaling during angiogenesis (PubMed:23708998). Binds polyubiquitin of different linkage types (PubMed:23708998). {ECO:0000269|PubMed:17006537, ECO:0000269|PubMed:19136968, ECO:0000269|PubMed:20005846, ECO:0000269|PubMed:21455173, ECO:0000269|PubMed:21455180, ECO:0000269|PubMed:21455181, ECO:0000269|PubMed:22863777, ECO:0000269|PubMed:23708998, ECO:0000269|PubMed:27458237, ECO:0000269|PubMed:28189684}.; ",{"$nulls":4},"p.Ser383Thr","c.1148G>C","MODERATE","383/1072",7,{"$nulls":5},"5","456","403","337","281","421","363","0","0","0","0.427",{"$nulls":20},"2.911369","0.97;1.03",".;1.87","0.828639","-0.84;-0.34","0.998;0.997","0.403;0.512","0.282;0.329",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","444,0","0","444","0/1","225,165","0.4231","390",null,"chr14:24150399:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4235"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","RNF31","chr14:24150399","RNF31(S383T)",null,null,"region of interest (Polyubiquitin-binding ), modified residue (Phosphoserine), splice variant (In isoform 2. )","modified-residue:Phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase component of the LUBAC complex which conjugates linear ('Met-1'-linked) polyubiquitin chains to substrates and plays a key role in NF-kappa-B activation and regulation of inflammation (PubMed:17006537, PubMed:19136968, PubMed:20005846, PubMed:21455173, PubMed:21455180, PubMed:21455181, PubMed:22863777, PubMed:28189684). LUBAC conjugates linear polyubiquitin to IKBKG and RIPK1 and is involved in activation of the canonical NF-kappa-B and the JNK signaling pathways (PubMed:17006537, PubMed:19136968, PubMed:20005846, PubMed:21455173, PubMed:21455180, PubMed:21455181, PubMed:22863777, PubMed:28189684). Linear ubiquitination mediated by the LUBAC complex interferes with TNF-induced cell death and thereby prevents inflammation (PubMed:21455173, PubMed:28189684). LUBAC is recruited to the TNF-R1 signaling complex (TNF-RSC) following polyubiquitination of TNF-RSC components by BIRC2 and/or BIRC3 and to conjugate linear polyubiquitin to IKBKG and possibly other components contributing to the stability of the complex (PubMed:20005846, PubMed:27458237). Together with OTULIN, the LUBAC complex regulates the canonical Wnt signaling during angiogenesis (PubMed:23708998). Binds polyubiquitin of different linkage types (PubMed:23708998). {ECO:0000269|PubMed:17006537, ECO:0000269|PubMed:19136968, ECO:0000269|PubMed:20005846, ECO:0000269|PubMed:21455173, ECO:0000269|PubMed:21455180, ECO:0000269|PubMed:21455181, ECO:0000269|PubMed:22863777, ECO:0000269|PubMed:23708998, ECO:0000269|PubMed:27458237, ECO:0000269|PubMed:28189684}.; ",{"$nulls":4},"p.Ser383Thr","c.1148G>C","MODERATE","383/1072",7,{"$nulls":5},"5","456","353","337","249","420","311","0","0","0","0.5627",{"$nulls":20},"2.911369","0.97;1.03",".;1.87","0.828639","-0.84;-0.34","0.998;0.997","0.403;0.512","0.282;0.329",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","444,0","0","444","0/1","147,180","0.5505","327",null,"chr14:24150399:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5261"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SALL1","chr16:51140208","SALL1(A672S)",{"$nulls":6},255,"PASS","Missense","rs1261072207",-1,"DISEASE: Townes-Brocks syndrome 1 (TBS1) [MIM:107480]: A form of Townes-Brocks syndrome, a rare autosomal dominant disease characterized by the triad of imperforate anus, dysplastic ears, and thumb malformations. Minor features of the condition include hearing loss, foot malformations, renal impairment with or without renal malformations, genitourinary malformations, and congenital heart disease. {ECO:0000269|PubMed:10533063, ECO:0000269|PubMed:9425907, ECO:0000269|PubMed:9973281}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some individuals with SALL1 mutations manifest a phenotype overlapping with TBS1 and bronchio-oto-renal syndrome. Clinical features include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux, hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or hand malformations of TBS1. {ECO:0000269|PubMed:10928856}.; ","FUNCTION: Transcriptional repressor involved in organogenesis. {ECO:0000250}.; ",{"$nulls":4},"p.Ala672Ser","c.2014G>T","MODERATE","672/1324",2,{"$nulls":5},"4","544","407","437","319","487","351","0.0018","0.0018","0","0.1168",{"$nulls":20},"2.200833","3.24;3.22;3.22",".;2.41;.","1","-1.33;-1.36;-1.33",".;0.635;.","0.042;0.046;0.054","0.271;0.252;.",{"$nulls":3},"Unknown",-1,"AD","Townes-Brocks syndrome","Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Renal",{"$nulls":3},"C4551481","0/0","539,1","0.0019","540","0/1","356,49","0.121","405",null,"chr16:51140208:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1191"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SALL1","chr16:51140208","SALL1(A672S)",{"$nulls":6},255,"PASS","Missense","rs1261072207",-1,"DISEASE: Townes-Brocks syndrome 1 (TBS1) [MIM:107480]: A form of Townes-Brocks syndrome, a rare autosomal dominant disease characterized by the triad of imperforate anus, dysplastic ears, and thumb malformations. Minor features of the condition include hearing loss, foot malformations, renal impairment with or without renal malformations, genitourinary malformations, and congenital heart disease. {ECO:0000269|PubMed:10533063, ECO:0000269|PubMed:9425907, ECO:0000269|PubMed:9973281}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some individuals with SALL1 mutations manifest a phenotype overlapping with TBS1 and bronchio-oto-renal syndrome. Clinical features include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux, hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or hand malformations of TBS1. {ECO:0000269|PubMed:10928856}.; ","FUNCTION: Transcriptional repressor involved in organogenesis. {ECO:0000250}.; ",{"$nulls":4},"p.Ala672Ser","c.2014G>T","MODERATE","672/1324",2,{"$nulls":5},"4","544","418","437","310","487","359","0.0018","0.0018","0","0.1727",{"$nulls":20},"2.200833","3.24;3.22;3.22",".;2.41;.","1","-1.33;-1.36;-1.33",".;0.635;.","0.042;0.046;0.054","0.271;0.252;.",{"$nulls":3},"Unknown",-1,"AD","Townes-Brocks syndrome","Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Renal",{"$nulls":3},"C4551481","0/0","539,1","0.0019","540","0/1","342,71","0.1719","413",null,"chr16:51140208:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1516"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SALL1","chr16:51140586","SALL1(P546A)",{"$nulls":6},255,"PASS","Missense","rs750142302",1.5000000000000002E-5,"DISEASE: Townes-Brocks syndrome 1 (TBS1) [MIM:107480]: A form of Townes-Brocks syndrome, a rare autosomal dominant disease characterized by the triad of imperforate anus, dysplastic ears, and thumb malformations. Minor features of the condition include hearing loss, foot malformations, renal impairment with or without renal malformations, genitourinary malformations, and congenital heart disease. {ECO:0000269|PubMed:10533063, ECO:0000269|PubMed:9425907, ECO:0000269|PubMed:9973281}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some individuals with SALL1 mutations manifest a phenotype overlapping with TBS1 and bronchio-oto-renal syndrome. Clinical features include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux, hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or hand malformations of TBS1. {ECO:0000269|PubMed:10928856}.; ","FUNCTION: Transcriptional repressor involved in organogenesis. {ECO:0000250}.; ",{"$nulls":4},"p.Pro546Ala","c.1636C>G","MODERATE","546/1324",2,{"$nulls":5},"5","495","368","402","286","449","329","0","0","0","0.1672",{"$nulls":20},"3.225838","2.94;2.97;2.91",".;2.83;.","1","-6.77;-6.47;-6.77",".;0.999;.","0.009;0.01;0.009","0.357;0.349;.",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,"AD","Townes-Brocks syndrome","Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Renal",{"$nulls":3},"C4551481","0/0","496,0","0","496","0/1","294,64","0.1788","358",null,"chr16:51140586:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1748"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SALL4","chr20:51790987","SALL4(T499M)",null,null,"splice variant (In isoform SALL4B. )",{"$nulls":3},255,"PASS","Missense","rs769115027",6.058e-05,"DISEASE: Duane-radial ray syndrome (DRRS) [MIM:607323]: Disorder characterized by the association of forearm malformations with Duane retraction syndrome. {ECO:0000269|PubMed:12393809, ECO:0000269|PubMed:12395297, ECO:0000269|PubMed:16402211}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Oculootoradial syndrome (OORS) [MIM:147750]: Autosomal dominant condition characterized by upper limbs anomalies (radial ray defects, carpal bones fusion), extraocular motor disturbances, congenital bilateral non-progressive mixed hearing loss. Other less consistent malformations include heart involvement, mild thrombocytopenia and leukocytosis (before age 50), shoulder girdle hypoplasia, imperforate anus, kidney malrotation or rectovaginal fistula. The IVIC syndrome is an allelic disorder of Duane-radial ray syndrome (DRRS) with a similar phenotype. {ECO:0000269|PubMed:17256792}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor with a key role in the maintenance and self-renewal of embryonic and hematopoietic stem cells. {ECO:0000269|PubMed:23012367}.; ",{"$nulls":4},"p.Thr499Met","c.1496C>T","MODERATE","499/1053",2,{"$nulls":5},"5","523","662","450","552","455","552","0","0","0","0.0888",{"$nulls":20},"-0.542922","3.02","-1.37","1","0.56",null,"0.263","0.074",{"$nulls":3},"ExAC_SAS_AF",6.058e-05,"AD","Duane-radial ray/Okohiro syndrome; Acro-Renal-Ocular syndrome","Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Musculoskeletal; Ophthalmologic; Renal",null,"The protein encoded by this gene may be a zinc finger transcription factor. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). [provided by RefSeq, Jul 2008].  ",null,"C1327918| C1623209","0/0","524,0","0","524","0/1","595,55","0.0846","650",null,"chr20:51790987:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0833"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SALL4","chr20:51790987","SALL4(T499M)",null,null,"splice variant (In isoform SALL4B. )",{"$nulls":3},255,"PASS","Missense","rs769115027",6.058e-05,"DISEASE: Duane-radial ray syndrome (DRRS) [MIM:607323]: Disorder characterized by the association of forearm malformations with Duane retraction syndrome. {ECO:0000269|PubMed:12393809, ECO:0000269|PubMed:12395297, ECO:0000269|PubMed:16402211}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Oculootoradial syndrome (OORS) [MIM:147750]: Autosomal dominant condition characterized by upper limbs anomalies (radial ray defects, carpal bones fusion), extraocular motor disturbances, congenital bilateral non-progressive mixed hearing loss. Other less consistent malformations include heart involvement, mild thrombocytopenia and leukocytosis (before age 50), shoulder girdle hypoplasia, imperforate anus, kidney malrotation or rectovaginal fistula. The IVIC syndrome is an allelic disorder of Duane-radial ray syndrome (DRRS) with a similar phenotype. {ECO:0000269|PubMed:17256792}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor with a key role in the maintenance and self-renewal of embryonic and hematopoietic stem cells. {ECO:0000269|PubMed:23012367}.; ",{"$nulls":4},"p.Thr499Met","c.1496C>T","MODERATE","499/1053",2,{"$nulls":5},"5","523","689","450","573","455","574","0","0","0","0.0679",{"$nulls":20},"-0.542922","3.02","-1.37","1","0.56",null,"0.263","0.074",{"$nulls":3},"ExAC_SAS_AF",6.058e-05,"AD","Duane-radial ray/Okohiro syndrome; Acro-Renal-Ocular syndrome","Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Musculoskeletal; Ophthalmologic; Renal",null,"The protein encoded by this gene may be a zinc finger transcription factor. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). [provided by RefSeq, Jul 2008].  ",null,"C1327918| C1623209","0/0","530,0","0","530","0/1","645,47","0.0679","692",null,"chr20:51790987:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0576"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SCN10A","chr3:38701857","SCN10A(V1547L)",{"$nulls":6},255,"PASS","Missense","rs377492327",2.2696323195642309E-4,"DISEASE: Episodic pain syndrome, familial, 2 (FEPS2) [MIM:615551]: An autosomal dominant neurologic disorder characterized by adult- onset of paroxysmal pain mainly affecting the distal lower extremities. {ECO:0000269|PubMed:23115331}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tetrodotoxin-resistant channel that mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium- selective channel through which sodium ions may pass in accordance with their electrochemical gradient. Plays a role in neuropathic pain mechanisms. {ECO:0000269|PubMed:9839820}.; ",{"$nulls":4},"p.Val1547Leu","c.4639G>T","MODERATE","1547/1956",26,{"$nulls":5},"5","340","273","280","231","277","232","0","0","0","0.1293",{"$nulls":20},"2.89512","-5.25;.;.;.","2.76;.;2.76;.","0.999767","-2.71;.;.;.","0.893;.;0.893;.","0.001;.;.;.","0.687;.;.;.",{"$nulls":3},"ESP6500_AA_AF",2.2696323195642309E-4,{"$nulls":6},"C3809893","0/0","330,0","0","330","0/1","238,36","0.1314","274",null,"chr3:38701857:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1212"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SCN10A","chr3:38701857","SCN10A(V1547L)",{"$nulls":6},255,"PASS","Missense","rs377492327",2.2696323195642309E-4,"DISEASE: Episodic pain syndrome, familial, 2 (FEPS2) [MIM:615551]: An autosomal dominant neurologic disorder characterized by adult- onset of paroxysmal pain mainly affecting the distal lower extremities. {ECO:0000269|PubMed:23115331}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tetrodotoxin-resistant channel that mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium- selective channel through which sodium ions may pass in accordance with their electrochemical gradient. Plays a role in neuropathic pain mechanisms. {ECO:0000269|PubMed:9839820}.; ",{"$nulls":4},"p.Val1547Leu","c.4639G>T","MODERATE","1547/1956",26,{"$nulls":5},"5","340","317","280","262","276","248","0","0","0","0.1371",{"$nulls":20},"2.89512","-5.25;.;.;.","2.76;.;2.76;.","0.999767","-2.71;.;.;.","0.893;.;0.893;.","0.001;.;.;.","0.687;.;.;.",{"$nulls":3},"ESP6500_AA_AF",2.2696323195642309E-4,{"$nulls":6},"C3809893","0/0","333,0","0","333","0/1","266,45","0.1447","311",null,"chr3:38701857:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1489"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SIGLEC12","chr19:51501733","SIGLEC12(Sequence Feature)",{"$nulls":3},"signal-peptide:match_to_sequence_model_evidence_used_in_manual_assertion","MODERATE",null,255,"PASS","Sequence Feature",null,-1,null,"FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface.; ",{"$nulls":5},"c.1A>C","MODERATE",null,1,{"$nulls":5},"5","444","462","339","328","418","411","0","0","0","0.1095",{"$nulls":20},"0.477335","1.11",null,"0.702588","-0.16","0.023",null,"0.598",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","437,0","0","437","0/1","393,49","0.1109","442",null,"chr19:51501733:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1067"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SLC16A12","chr10:89439173","SLC16A12(F153L)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Proton-linked monocarboxylate transporter that mediates creatine transport across the plasma membrane. {ECO:0000269|PubMed:23578822}.; ",{"$nulls":4},"p.Phe153Leu","c.459T>A","MODERATE","153/516",6,{"$nulls":5},"5","280","241","203","172","259","218","0","0","0","0.133",{"$nulls":20},"3.822623","1.73",null,"0.999945","-1.65",null,"0.178","0.641",{"$nulls":3},"Unknown",-1,"AD","Cataract, juvenile, with microcornea and glucosuria","Biochemical; Renal",null,"This gene encodes a transmembrane transporter that likely plays a role in monocarboxylic acid transport. A mutation in this gene has been associated with juvenile cataracts with microcornea and renal glucosuria. [provided by RefSeq, Mar 2010].  ",null,"C4310806","0/0","278,0","0","278","0/1","204,33","0.1392","237",null,"chr10:89439173:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.157"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SLFN12L","chr17:35479155","SLFN12L(E381V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu381Val","c.1142A>T","MODERATE","381/617",3,{"$nulls":5},"5","620","479","463","335","561","424","0.0016","0.0016","0","0.4269",{"$nulls":20},"-0.574983","0.65;0.65;.","-0.55;.;.","1","0.43;0.43;.",".;0.001;.","0.412;0.033;.","0.152;0.146;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","616,1","0.0016","617","0/1","255,187","0.4231","442",null,"chr17:35479155:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4179"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SLFN12L","chr17:35479155","SLFN12L(E381V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu381Val","c.1142A>T","MODERATE","381/617",3,{"$nulls":5},"5","620","540","463","386","559","484","0.0016","0.0016","0","0.6095",{"$nulls":20},"-0.574983","0.65;0.65;.","-0.55;.;.","1","0.43;0.43;.",".;0.001;.","0.412;0.033;.","0.152;0.146;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","615,1","0.0016","616","0/1","215,307","0.5881","522",null,"chr17:35479155:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5803"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SNX5","chr20:17955411","SNX5(W74*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)) or phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) (PubMed:15561769). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Does not have in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Involved in retrograde transport of lysosomal enzyme receptor IGF2R (PubMed:17148574, PubMed:18596235). May function as link between endosomal transport vesicles and dynactin (Probable). Plays a role in the internalization of EGFR after EGF stimulation (Probable). Involved in EGFR endosomal sorting and degradation; the function involves PIP5K1C isoform 3 and is retromer-independent (PubMed:23602387). Together with PIP5K1C isoform 3 facilitates HGS interaction with ubiquitinated EGFR, which initiates EGFR sorting to intraluminal vesicles (ILVs) of the multivesicular body for subsequent lysosomal degradation (Probable). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). Plays a role in macropinocytosis (PubMed:18854019, PubMed:21048941). {ECO:0000269|PubMed:18854019, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:24610942, ECO:0000303|PubMed:15561769, ECO:0000303|PubMed:19619496, ECO:0000303|PubMed:23085988}.; ",{"$nulls":4},"p.Trp74*","c.221G>A","HIGH","74/404",3,{"$nulls":5},"4","369","318","296","242","291","183","0","0","0","0.153",{"$nulls":5},"(SNX5|ENSG00000089006|1|1.00)","(SNX5|ENSG00000089006|1|1.00)",{"$nulls":13},"7.901831",null,null,"1",{"$nulls":3},"0.867;0.867;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","367,0","0","367","0/1","266,42","0.1364","308",null,"chr20:17955411:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1405"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SRP68","chr17:76067305","SRP68(R93C)",{"$nulls":6},255,"PASS","Missense","rs780073296",1.7270000000000002E-4,null,"FUNCTION: Signal-recognition-particle assembly has a crucial role in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP68 binds the 7S RNA, SRP72 binds to this complex subsequently. This ribonucleoprotein complex might interact directly with the docking protein in the ER membrane and possibly participate in the elongation arrest function.; ",{"$nulls":4},"p.Arg93Cys","c.277C>T","MODERATE","93/627",3,1,{"$nulls":4},"5","445","339","311","234","411","319","0","0","0","0.4107",{"$nulls":20},"4.42111",null,"3.255","1","-6.99","1.0",null,"0.775",{"$nulls":3},"ExAC_AMR_AF",1.7270000000000002E-4,{"$nulls":7},"0/0","432,0","0","432","0/1","195,142","0.4214","337",null,"chr17:76067305:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.406"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SRP68","chr17:76067305","SRP68(R93C)",{"$nulls":6},255,"PASS","Missense","rs780073296",1.7270000000000002E-4,null,"FUNCTION: Signal-recognition-particle assembly has a crucial role in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP68 binds the 7S RNA, SRP72 binds to this complex subsequently. This ribonucleoprotein complex might interact directly with the docking protein in the ER membrane and possibly participate in the elongation arrest function.; ",{"$nulls":4},"p.Arg93Cys","c.277C>T","MODERATE","93/627",3,1,{"$nulls":4},"5","445","424","311","286","412","378","0","0","0","0.5873",{"$nulls":20},"4.42111",null,"3.255","1","-6.99","1.0",null,"0.775",{"$nulls":3},"ExAC_AMR_AF",1.7270000000000002E-4,{"$nulls":7},"0/0","432,0","0","432","0/1","166,240","0.5911","406",null,"chr17:76067305:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5839"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SSTR5","chr16:1078907","SSTR5(Sequence Feature)",{"$nulls":3},"glycosylation-site:N-linked_(GlcNAc...)","MODERATE",null,255,"PASS","Sequence Feature","rs761846302",-1,null,"FUNCTION: Receptor for somatostatin 28 and to a lesser extent for somatostatin-14. The activity of this receptor is mediated by G proteins which inhibit adenylyl cyclase. Increases cell growth inhibition activity of SSTR2 following heterodimerization. {ECO:0000269|PubMed:12072395, ECO:0000269|PubMed:7908405, ECO:0000269|PubMed:8078491, ECO:0000269|PubMed:8373420}.; ",{"$nulls":5},"c.39C>T","MODERATE",null,1,{"$nulls":5},"5","261","203","177","143","236","182","0","0","0","0.1484",{"$nulls":31},"Unknown",-1,"AD","Resistance to somatostatin treatment","General",{"$nulls":4},"0/0","257,0","0","257","0/1","165,35","0.175","200",null,"chr16:1078907:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1958"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SSTR5","chr16:1078907","SSTR5(Sequence Feature)",{"$nulls":3},"glycosylation-site:N-linked_(GlcNAc...)","MODERATE",null,255,"PASS","Sequence Feature","rs761846302",-1,null,"FUNCTION: Receptor for somatostatin 28 and to a lesser extent for somatostatin-14. The activity of this receptor is mediated by G proteins which inhibit adenylyl cyclase. Increases cell growth inhibition activity of SSTR2 following heterodimerization. {ECO:0000269|PubMed:12072395, ECO:0000269|PubMed:7908405, ECO:0000269|PubMed:8078491, ECO:0000269|PubMed:8373420}.; ",{"$nulls":5},"c.39C>T","MODERATE",null,1,{"$nulls":5},"5","261","210","177","143","235","190","0","0","0","0.1684",{"$nulls":31},"Unknown",-1,"AD","Resistance to somatostatin treatment","General",{"$nulls":4},"0/0","257,0","0","257","0/1","164,34","0.1717","198",null,"chr16:1078907:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1608"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","SYF2","chr1:25228181","SYF2(A105T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.; ",{"$nulls":4},"p.Ala105Thr","c.313G>A","MODERATE","105/243",4,{"$nulls":5},"4","579","524",null,null,"523","474","0.0017","0.0017","0","0.0527",{"$nulls":20},"3.837096","0.69;0.82","3.4;.","1","-3.86","1.0;.","0.004","0.897;0.867",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","548,1","0.0018","549","0/1","448,28","0.0588","476",null,"chr1:25228181:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","SYT6","chr1:114093805","SYT6(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. May mediate Ca(2+)- regulation of exocytosis in acrosomal reaction in sperm (By similarity). {ECO:0000250|UniProtKB:Q9R0N8}.; ",{"$nulls":5},"c.1516-2A>G","HIGH",null,6,{"$nulls":5},"5","382","375","279","274","326","315","0","0","0","0.1016",{"$nulls":20},"4.53737",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","378,0","0","378","0/1","331,39","0.1054","370",null,"chr1:114093805:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1022"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","TEP1","chr14:20403770","TEP1(R383W)",null,null,"domain (TROVE )",{"$nulls":3},255,"PASS","Missense","rs914900744",-1,null,"FUNCTION: Component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini (PubMed:19179534). Also component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport (By similarity). Responsible for the localizing and stabilizing vault RNA (vRNA) association in the vault ribonucleoprotein particle. Binds to TERC (By similarity). {ECO:0000250|UniProtKB:P97499, ECO:0000269|PubMed:19179534}.; ",{"$nulls":4},"p.Arg383Trp","c.1147C>T","MODERATE","383/2627",6,1,{"$nulls":4},"5","695","466","517","353","564","389","0","0","0","0.4859",{"$nulls":20},"3.254574","0.59","2.215","0.969991;1","-3.13","0.589","0.071","0.365",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","683,0","0","683","0/1","256,193","0.4298","449",null,"chr14:20403770:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4334"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TEP1","chr14:20403770","TEP1(R383W)",null,null,"domain (TROVE )",{"$nulls":3},255,"PASS","Missense","rs914900744",-1,null,"FUNCTION: Component of the telomerase ribonucleoprotein complex that is essential for the replication of chromosome termini (PubMed:19179534). Also component of the ribonucleoprotein vaults particle, a multi-subunit structure involved in nucleo-cytoplasmic transport (By similarity). Responsible for the localizing and stabilizing vault RNA (vRNA) association in the vault ribonucleoprotein particle. Binds to TERC (By similarity). {ECO:0000250|UniProtKB:P97499, ECO:0000269|PubMed:19179534}.; ",{"$nulls":4},"p.Arg383Trp","c.1147C>T","MODERATE","383/2627",6,1,{"$nulls":4},"5","695","467","517","326","566","397","0","0","0","0.6146",{"$nulls":20},"3.254574","0.59","2.215","0.969991;1","-3.13","0.589","0.071","0.365",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","683,0","0","683","0/1","185,259","0.5833","444",null,"chr14:20403770:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5675"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TET1","chr10:68686354","TET1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,"DISEASE: Note=A chromosomal aberration involving TET1 may be a cause of acute leukemias (PubMed:12646957). Translocation t(10;11)(q22;q23) with KMT2A/MLL1. This is a rare chromosomal translocation 5' KMT2A/MLL1-TET1 3' (PubMed:12124344, PubMed:12646957). {ECO:0000269|PubMed:12124344, ECO:0000269|PubMed:12646957}.; ","FUNCTION: Dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5- hydroxymethylcytosine (5hmC) and plays a key role in active DNA demethylation. Also mediates subsequent conversion of 5hmC into 5- formylcytosine (5fC), and conversion of 5fC to 5-carboxylcytosine (5caC). Conversion of 5mC into 5hmC, 5fC and 5caC probably constitutes the first step in cytosine demethylation. Methylation at the C5 position of cytosine bases is an epigenetic modification of the mammalian genome which plays an important role in transcriptional regulation. In addition to its role in DNA demethylation, plays a more general role in chromatin regulation. Preferentially binds to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Involved in the recruitment of the O-GlcNAc transferase OGT to CpG-rich transcription start sites of active genes, thereby promoting histone H2B GlcNAcylation by OGT. Also involved in transcription repression of a subset of genes through recruitment of transcriptional repressors to promoters. Involved in the balance between pluripotency and lineage commitment of cells it plays a role in embryonic stem cells maintenance and inner cell mass cell specification. Plays an important role in the tumorigenicity of glioblastoma cells. TET1-mediated production of 5hmC acts as a recruitment signal for the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789). {ECO:0000269|PubMed:12124344, ECO:0000269|PubMed:19372391, ECO:0000269|PubMed:19372393, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:21778364, ECO:0000269|PubMed:25284789}.; ",{"$nulls":5},"c.5053-2A>G","HIGH",null,10,{"$nulls":5},"4","280","205",null,null,"224","166","0","0","0","0.0904",{"$nulls":5},"(TET1|ENSG00000138336|1|1.00)",{"$nulls":14},"5.79665",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","279,0","0","279","0/1","185,16","0.0796","201",null,"chr10:68686354:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","THBS2","chr6:169234785","THBS2(V534M)",null,null,"domain (TSP type-1 3 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs147420892",0.000992063492063492,null,"FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Ligand for CD36 mediating antiangiogenic properties. {ECO:0000269|PubMed:20714802}.; ","level2",{"$nulls":3},"p.Val534Met","c.1600G>A","MODERATE","534/1172",11,1,{"$nulls":4},"5","416","345","277","238","350","301","0","0","0","0.1761",{"$nulls":20},"2.370492","0.61;.;.","2.435;.;2.435","0.996281","-0.42;.;.","0.493;.;0.493","0.027;.;.","0.358;.;0.36",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":3},"kTGF_BETA",null,null,"C0158252","0/0","383,0","0","383","0/1","272,61","0.1832","333",null,"chr6:169234785:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1597"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","THBS2","chr6:169234785","THBS2(V534M)",null,null,"domain (TSP type-1 3 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs147420892",0.000992063492063492,null,"FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Ligand for CD36 mediating antiangiogenic properties. {ECO:0000269|PubMed:20714802}.; ","level2",{"$nulls":3},"p.Val534Met","c.1600G>A","MODERATE","534/1172",11,1,{"$nulls":4},"5","416","355","277","244","347","289","0","0","0","0.0934",{"$nulls":20},"2.370492","0.61;.;.","2.435;.;2.435","0.996281","-0.42;.;.","0.493;.;0.493","0.027;.;.","0.358;.;0.36",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":3},"kTGF_BETA",null,null,"C0158252","0/0","399,0","0","399","0/1","303,35","0.1036","338",null,"chr6:169234785:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0902"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TOP2B","chr3:25601139","TOP2B(S1526P)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,"DISEASE: Note=A defect in TOP2B is associated with autism spectrum disorder (ASD). {ECO:0000269|PubMed:28343847}.; ","FUNCTION: Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. {ECO:0000269|PubMed:10684600}.; ","level2",{"$nulls":3},"p.Ser1526Pro","c.4576T>C","MODERATE","1526/1626",34,{"$nulls":5},"5","580","573","407","402","500","493","0","0","0","0.0751",{"$nulls":20},"3.507529","0.74","0.975;.","0.999995;0.999998;0.999995;0.999995","-1.75","0.822;0.787","0.093","0.56;0.658",{"$nulls":3},"Unknown",-1,{"$nulls":3},"dcPGX","This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This nuclear enzyme is involved in processes such as chromosome condensation, chromatid separation, and the relief of torsional stress that occurs during DNA transcription and replication. It catalyzes the transient breaking and rejoining of two strands of duplex DNA which allows the strands to pass through one another, thus altering the topology of DNA. Two forms of this enzyme exist as likely products of a gene duplication event. The gene encoding this form, beta, is localized to chromosome 3 and the alpha form is localized to chromosome 17. The gene encoding this enzyme functions as the target for several anticancer agents and a variety of mutations in this gene have been associated with the development of drug resistance. Reduced activity of this enzyme may also play a role in ataxia-telangiectasia. Alternative splicing of this gene results in two transcript variants; however, the second variant has not yet been fully described. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","560,0","0","560","0/1","499,39","0.0725","538",null,"chr3:25601139:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0771"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","TP53","chr17:7670694","TP53(F299fs)",null,null,"region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), sequence variant (In sporadic cancers; somatic mutation. TP53(L299P)), sequence variant (In sporadic cancers; somatic mutation. TP53(L299Q)), sequence variant (In a sporadic cancer; somatic mutation. TP53(L299R)), sequence variant (In a sporadic cancer; somatic mutation. TP53(L299V))",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Phe299fs","c.897delC","HIGH","299/410",10,1,{"$nulls":4},"5","476","348","330","227","401","300","0","0","0","0.4133",{"$nulls":5},"(TP53|ENSG00000141510|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","441,0","0","441","0/1","182,135","0.4259","317",null,"chr17:7670694:CG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4273"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TP53","chr17:7670694","TP53(F299fs)",null,null,"region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), sequence variant (In sporadic cancers; somatic mutation. TP53(L299P)), sequence variant (In sporadic cancers; somatic mutation. TP53(L299Q)), sequence variant (In a sporadic cancer; somatic mutation. TP53(L299R)), sequence variant (In a sporadic cancer; somatic mutation. TP53(L299V))",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Phe299fs","c.897delC","HIGH","299/410",10,1,{"$nulls":4},"5","476","366","330","240","401","314","0","0","0","0.5064",{"$nulls":5},"(TP53|ENSG00000141510|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","441,0","0","441","0/1","146,184","0.5576","330",null,"chr17:7670694:CG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5625"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","TPH1","chr11:18022905","TPH1(V351V)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,{"$nulls":7},"c.1053A>T","HIGH",null,9,{"$nulls":5},"5","318","269","216","173","296","249","0","0","0","0.2892",{"$nulls":31},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the aromatic amino acid hydroxylase family. The encoded protein catalyzes the first and rate limiting step in the biosynthesis of serotonin, an important hormone and neurotransmitter. Mutations in this gene have been associated with an elevated risk for a variety of diseases and disorders, including schizophrenia, somatic anxiety, anger-related traits, bipolar disorder, suicidal behavior, addictions, and others.[provided by RefSeq, Apr 2009].  ",null,null,"0/0","317,0","0","317","0/1","188,76","0.2879","264",null,"chr11:18022905:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2832"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TPH1","chr11:18022905","TPH1(V351V)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,{"$nulls":7},"c.1053A>T","HIGH",null,9,{"$nulls":5},"5","318","319","216","204","295","288","0","0","0","0.3646",{"$nulls":31},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the aromatic amino acid hydroxylase family. The encoded protein catalyzes the first and rate limiting step in the biosynthesis of serotonin, an important hormone and neurotransmitter. Mutations in this gene have been associated with an elevated risk for a variety of diseases and disorders, including schizophrenia, somatic anxiety, anger-related traits, bipolar disorder, suicidal behavior, addictions, and others.[provided by RefSeq, Apr 2009].  ",null,null,"0/0","313,0","0","313","0/1","193,105","0.3523","298",null,"chr11:18022905:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.348"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TRIM46","chr1:155179702","TRIM46(H455fs)",null,null,"domain (Fibronectin type-III ), splice variant (In isoform 3 and isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function","rs760983049",-1,null,"FUNCTION: Microtubule-associated protein that is involved in the formation of parallel microtubule bundles linked by cross-bridges in the proximal axon. Required for the uniform orientation and maintenance of the parallel microtubule fascicles, which are important for efficient cargo delivery and trafficking in axons. Thereby also required for proper axon specification, the establishment of neuronal polarity and proper neuronal migration. {ECO:0000250|UniProtKB:Q7TNM2}.; ",{"$nulls":4},"p.His455fs","c.1363dupC","HIGH","455/759",8,{"$nulls":5},"4",null,null,"464","660","534","814",null,null,"0","0.0577",{"$nulls":5},"(TRIM46|ENSG00000163462|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","544,0","0","544","0/1","767,50","0.0612","817",null,"chr1:155179702:G:GC",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0606"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","TTC7A","chr2:47005997","TTC7A(A381S)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:24417819). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, plays a central role in bridging PI4KA to EFR3B and FAM126A, via direct interactions (By similarity). {ECO:0000250|UniProtKB:Q86TV6, ECO:0000269|PubMed:23229899, ECO:0000269|PubMed:24417819}.; ",{"$nulls":4},"p.Ala381Ser","c.1141G>T","MODERATE","381/882",9,{"$nulls":5},"5","835","779","618","555","729","680","0","0","0","0.0956",{"$nulls":20},"1.626992","0.62",".;1.465;1.465","0.745063","-1.71;-1.71;-1.81","0.153;0.165;.","0.126;0.144;0.145","0.342;0.334;0.312",{"$nulls":3},"Unknown",-1,"AR","Intestinal atresia, multiple","Allergy/Immunology/Infectious; Gastrointestinal",{"$nulls":3},"C0220744","0/0","812,0","0","812","0/1","664,74","0.1003","738",null,"chr2:47005997:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1063"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","TTC7A","chr2:47005997","TTC7A(A381S)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane (PubMed:23229899, PubMed:24417819). The complex acts as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) synthesis (Probable). In the complex, plays a central role in bridging PI4KA to EFR3B and FAM126A, via direct interactions (By similarity). {ECO:0000250|UniProtKB:Q86TV6, ECO:0000269|PubMed:23229899, ECO:0000269|PubMed:24417819}.; ",{"$nulls":4},"p.Ala381Ser","c.1141G>T","MODERATE","381/882",9,{"$nulls":5},"5","835","666","618","473","727","565","0","0","0","0.1186",{"$nulls":20},"1.626992","0.62",".;1.465;1.465","0.745063","-1.71;-1.71;-1.81","0.153;0.165;.","0.126;0.144;0.145","0.342;0.334;0.312",{"$nulls":3},"Unknown",-1,"AR","Intestinal atresia, multiple","Allergy/Immunology/Infectious; Gastrointestinal",{"$nulls":3},"C0220744","0/0","818,0","0","818","0/1","541,81","0.1302","622",null,"chr2:47005997:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1226"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","VWA5B2","chr3:184241246","VWA5B2(R1008C)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg1008Cys","c.3022C>T","MODERATE","1008/1242",18,{"$nulls":5},"4","740","831","565","622","656","723","0","0","0","0.0678",{"$nulls":20},"-0.285314","2.85;2.17",null,"0.999999;1;1","-0.2",".;0.001","0.092;0.09","0.044;0.039",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","725,0","0","725","0/1","749,61","0.0753","810",null,"chr3:184241246:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.074"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","VWA5B2","chr3:184241246","VWA5B2(R1008C)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg1008Cys","c.3022C>T","MODERATE","1008/1242",18,{"$nulls":5},"4","740","884","565","687","657","778","0","0","0","0.0835",{"$nulls":20},"-0.285314","2.85;2.17",null,"0.999999;1;1","-0.2",".;0.001","0.092;0.09","0.044;0.039",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","726,0","0","726","0/1","777,74","0.087","851",null,"chr3:184241246:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0946"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","WDR53","chr3:196554248","WDR53(T347S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr347Ser","c.1040C>G","MODERATE","347/358",4,{"$nulls":5},"4","185","258",null,null,"155","218","0","0","0","0.1606",{"$nulls":20},"1.5422099999999999","-0.37;1.63;1.6","1.2;.;.","0.780264","0.26;0.66;0.66","0.022;.;.","0.808;0.895;0.889","0.077;0.092;0.082",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","189,0","0","189","0/1","221,39","0.15","260",null,"chr3:196554248:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","XIRP1","chr3:39189006","XIRP1(Q147L)",null,null,"splice variant (In isoform C. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Protects actin filaments from depolymerization. {ECO:0000269|PubMed:15454575}.; ",{"$nulls":4},"p.Gln147Leu","c.440A>T","MODERATE","147/1843",2,{"$nulls":5},"4","332","276","271","216","281","243","0","0","0","0.1276",{"$nulls":20},"-0.268193","3.46;3.85","1.32","1;1;0.999999","-3.16","0.055;0.003","0.106;0.14","0.06;0.097",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","340,0","0","340","0/1","242,34","0.1232","276",null,"chr3:39189006:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1343"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","XKR9","chr8:70734273","XKR9(I325fs)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ile325fs","c.972_975delTATA","HIGH","324/373",5,{"$nulls":5},"3",null,null,"190","359",{"$nulls":11},"(XKR9|ENSG00000221947|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","270,0","0","270","0/1","504,29","0.0544","533",null,"chr8:70734273:CTATA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0557"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","XKR9","chr8:70734273","XKR9(I325fs)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ile325fs","c.972_975delTATA","HIGH","324/373",5,{"$nulls":5},"3",null,null,"190","348",{"$nulls":11},"(XKR9|ENSG00000221947|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","269,0","0","269","0/1","470,28","0.0562","498",null,"chr8:70734273:CTATA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0575"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","YBEY","chr21:46291375","YBEY(D84E)",null,null,"splice variant (In isoform D. ), splice variant (In isoform B. )","antibody-mapping:heterologous_protein_expression_evidence","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Single strand-specific metallo-endoribonuclease involved in rRNA maturation. {ECO:0000305|PubMed:28153719}.; ",{"$nulls":4},"p.Asp84Glu","c.252T>G","MODERATE","84/167",3,{"$nulls":5},"5","286","414","232","314","241","349","0","0","0","0.0774",{"$nulls":20},"1.806727",null,"0.96;.;0.96;0.96","0.990692;0.990692;0.990692;0.990692;1;1","-0.94;-1.31;-0.94;-0.94","0.034;0.096;0.034;0.034","0.24;0.197;0.24;0.24","0.273;0.304;0.249;0.249",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","282,0","0","282","0/1","352,31","0.0809","383",null,"chr21:46291375:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0764"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ZBTB20","chr3:114350790","ZBTB20(A430T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Primrose syndrome (PRIMS) [MIM:259050]: A disease characterized by macrocephaly, intellectual disability, disturbed behavior, dysmorphic facial features, ectopic calcifications, large calcified ear auricles, and progressive muscle wasting. {ECO:0000269|PubMed:25017102}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses (PubMed:11352661). Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal (By similarity). {ECO:0000250|UniProtKB:Q8K0L9, ECO:0000269|PubMed:11352661}.; ",{"$nulls":4},"p.Ala430Thr","c.1288G>A","MODERATE","430/741",4,{"$nulls":5},"5","737","549","580","425","628","483","0","0","0","0.1532",{"$nulls":20},"1.533849","2.93;2.93;2.93;2.93;2.93;2.91;2.93",".;.;.;.;.;0;.","0.577688","-0.68;-0.68;-0.68;-0.68;-0.68;-0.69;-0.68",".;.;.;.;.;0.002;.","0.086;0.086;0.086;0.086;0.086;0.052;0.086","0.108;0.114;0.109;0.109;0.114;0.069;0.15",{"$nulls":3},"Unknown",-1,"AD","Primrose syndrome","Craniofacial; Dermatologic; Musculoskeletal; Neurologic",{"$nulls":3},"C0796121","0/0","733,0","0","733","0/1","453,92","0.1688","545",null,"chr3:114350790:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1812"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ZBTB20","chr3:114350790","ZBTB20(A430T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Primrose syndrome (PRIMS) [MIM:259050]: A disease characterized by macrocephaly, intellectual disability, disturbed behavior, dysmorphic facial features, ectopic calcifications, large calcified ear auricles, and progressive muscle wasting. {ECO:0000269|PubMed:25017102}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a transcription factor that may be involved in hematopoiesis, oncogenesis, and immune responses (PubMed:11352661). Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal (By similarity). {ECO:0000250|UniProtKB:Q8K0L9, ECO:0000269|PubMed:11352661}.; ",{"$nulls":4},"p.Ala430Thr","c.1288G>A","MODERATE","430/741",4,{"$nulls":5},"5","737","463","580","365","628","397","0","0","0","0.33",{"$nulls":20},"1.533849","2.93;2.93;2.93;2.93;2.93;2.91;2.93",".;.;.;.;.;0;.","0.577688","-0.68;-0.68;-0.68;-0.68;-0.68;-0.69;-0.68",".;.;.;.;.;0.002;.","0.086;0.086;0.086;0.086;0.086;0.052;0.086","0.108;0.114;0.109;0.109;0.114;0.069;0.15",{"$nulls":3},"Unknown",-1,"AD","Primrose syndrome","Craniofacial; Dermatologic; Musculoskeletal; Neurologic",{"$nulls":3},"C0796121","0/0","734,0","0","734","0/1","298,160","0.3493","458",null,"chr3:114350790:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3479"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ZFP82","chr19:36393663","ZFP82(Y226F)",null,null,"zinc finger region (C2H2-type 3 )","zinc-finger-region:C2H2-type_3","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Tyr226Phe","c.677A>T","MODERATE","226/532",5,{"$nulls":5},"5","515","473","365","305","383","335","0","0","0","0.2149",{"$nulls":20},"2.315521","2.22","0.345","0.999888","-2.3","0.804","0.197","0.183",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","517,0","0","517","0/1","357,106","0.2289","463",null,"chr19:36393663:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2492"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ZFP82","chr19:36393663","ZFP82(Y226F)",null,null,"zinc finger region (C2H2-type 3 )","zinc-finger-region:C2H2-type_3","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Tyr226Phe","c.677A>T","MODERATE","226/532",5,{"$nulls":5},"5","515","521","365","364","383","369","0","0","0","0.2764",{"$nulls":20},"2.315521","2.22","0.345","0.999888","-2.3","0.804","0.197","0.183",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","516,0","0","516","0/1","358,144","0.2869","502",null,"chr19:36393663:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2802"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ZNF175","chr19:51587020","ZNF175(G230A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Down-regulates the expression of several chemokine receptors. Interferes with HIV-1 replication by suppressing Tat- induced viral LTR promoter activity. {ECO:0000269|PubMed:14688346}.; ",{"$nulls":4},"p.Gly230Ala","c.689G>C","MODERATE","230/711",5,{"$nulls":5},"5","596","543","470","426","502","441","0","0","0","0.0998",{"$nulls":20},"1.026884","3.31","1.15","1;0.999998","-2.54","0.673","0.002","0.131",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","590,0","0","590","0/1","482,48","0.0906","530",null,"chr19:51587020:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0962"]
["08DJ","T12","JLPIKTOR_JLPIKTOR_17113008DJ","ZNF175","chr19:51587020","ZNF175(G230A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Down-regulates the expression of several chemokine receptors. Interferes with HIV-1 replication by suppressing Tat- induced viral LTR promoter activity. {ECO:0000269|PubMed:14688346}.; ",{"$nulls":4},"p.Gly230Ala","c.689G>C","MODERATE","230/711",5,{"$nulls":5},"5","596","479","470","368","500","399","0","0","0","0.1378",{"$nulls":20},"1.026884","3.31","1.15","1;0.999998","-2.54","0.673","0.002","0.131",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","593,0","0","593","0/1","408,62","0.1319","470",null,"chr19:51587020:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1223"]
["08DJ","T11","JLPIKTOR_JLPIKTOR_17113008DJ","ZNF708","chr19:21294491","ZNF708(K159*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys159*","c.475A>T","HIGH","159/563",4,{"$nulls":5},"5","120","121","100","105","65","78","0","0","0","0.0641",{"$nulls":20},"3.8996969999999997",null,null,"1",{"$nulls":3},"0.023;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","117,0","0","117","0/1","110,12","0.0984","122",null,"chr19:21294491:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113008DJ","somatic","somatic","JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113008DJ/somatic/JLPIKTOR_17113008DJ_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113008DJ_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0857"]

{"sheet":"09JM","index":6,"n_rows":93,"n_cols":107,"rows_kept":93}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","APOBEC3A","chr22:38957705","APOBEC3A(P5L)",{"$nulls":6},255,"PASS","Missense","rs1375973535",-1,null,"FUNCTION: DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno- associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. {ECO:0000269|PubMed:10469298, ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:19461882, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:20615867, ECO:0000269|PubMed:21123384, ECO:0000269|PubMed:21368204, ECO:0000269|PubMed:21460793, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:22457529, ECO:0000269|PubMed:22896697}.; ",{"$nulls":4},"p.Pro5Leu","c.14C>T","MODERATE","5/199",1,{"$nulls":5},"5","464","394","305","278","442","369","0","0","0","0.0921",{"$nulls":20},"0.824342","-0.1;-0.1;.","2.595","1","1.0;1.0;.","0.007","0.389;0.389;.","0.109;0.085;0.085",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","445,0","0","445","0/1","334,35","0.0949","369",null,"chr22:38957705:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0971"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","AQR","chr15:34906595","AQR(G594D)",null,null,"region of interest (Required for assembly of the IB complex ), strand ",{"$nulls":3},255,"PASS","Missense","rs368977117",1.201923076923077E-4,null,"FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:25599396, PubMed:28502770, PubMed:28076346). Intron-binding spliceosomal protein required to link pre-mRNA splicing and snoRNP (small nucleolar ribonucleoprotein) biogenesis (PubMed:16949364). Plays a key role in position-dependent assembly of intron-encoded box C/D small snoRNP, splicing being required for snoRNP assembly (PubMed:16949364). May act by helping the folding of the snoRNA sequence. Binds to intron of pre-mRNAs in a sequence-independent manner, contacting the region between snoRNA and the branchpoint of introns (40 nucleotides upstream of the branchpoint) during the late stages of splicing (PubMed:16949364). Has ATP-dependent RNA helicase activity and can unwind double-stranded RNA molecules with a 3' overhang (in vitro) (PubMed:25599396). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:16949364, ECO:0000269|PubMed:25599396, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.; ",{"$nulls":4},"p.Gly594Asp","c.1781G>A","MODERATE","594/1485",18,{"$nulls":5},"3","583","433",{"$nulls":4},"0.0017","0.0017",{"$nulls":22},"3.914523","-3.64","3.225","1","-6.63","1.0",null,"0.943",{"$nulls":3},"ESP6500_EA_AF",1.201923076923077E-4,{"$nulls":7},"0/0","569,1","0.0018","570","0/1","380,43","0.1017","423",null,"chr15:34906595:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ARHGAP22","chr10:48450589","ARHGAP22(G530R)",null,null,"compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Missense","rs879703696",-1,null,"FUNCTION: Rho GTPase-activating protein involved in the signal transduction pathway that regulates endothelial cell capillary tube formation during angiogenesis. Acts as a GTPase activator for the RAC1 by converting it to an inactive GDP-bound state. Inhibits RAC1-dependent lamellipodia formation. May also play a role in transcription regulation via its interaction with VEZF1, by regulating activity of the endothelin-1 (EDN1) promoter (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly530Arg","c.1588G>A","MODERATE","530/714",9,{"$nulls":5},"4","639","474","574","418","510","384","0","0","0","0.1068",{"$nulls":20},"0.636459","2.95;2.23;1.85;2.62;2.62;2.92;2.95","0.695;.;.;.;.;.;.","1","-0.01;-0.46;-0.41;-0.21;-0.21;-0.01;-0.01","0.003;0.196;.;.;0.005;.;0.005","0.437;0.011;0.257;0.17;0.185;0.337;0.432","0.076;0.125;0.101;0.103;0.08;0.08;0.082",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","633,0","0","633","0/1","424,45","0.0959","469",null,"chr10:48450589:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1029"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ARX","chrX:25007371","ARX(G397fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Epileptic encephalopathy, early infantile, 1 (EIEE1) [MIM:308350]: A severe form of epilepsy characterized by frequent tonic seizures or spasms beginning in infancy with a specific EEG finding of suppression-burst patterns, characterized by high- voltage bursts alternating with almost flat suppression phases. Patients may progress to West syndrome, which is characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on EEG. {ECO:0000269|PubMed:11889467, ECO:0000269|PubMed:12376946, ECO:0000269|PubMed:27864847}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Partington syndrome (PRTS) [MIM:309510]: Characterized by mental retardation, episodic dystonic hand movements, and dysarthria. {ECO:0000269|PubMed:11889467}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, X-linked, ARX-related (MRXARX) [MIM:300419]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269|PubMed:11971879}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Agenesis of the corpus callosum, with abnormal genitalia (ACCAG) [MIM:300004]: A X-linked syndrome with variable expression in females. It is characterized by agenesis of corpus callosum, mental retardation and seizures. Manifestations in surviving males include severe acquired micrencephaly, mental retardation, limb contractures, scoliosis, tapered fingers with hyperconvex nails, a characteristic face with large eyes, prominent supraorbital ridges, synophrys, optic atrophy, broad alveolar ridges, and seizures. Urologic anomalies include renal dysplasia, cryptorchidism, and hypospadias. {ECO:0000269|PubMed:14722918}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcription factor required for normal brain development. May be important for maintenance of specific neuronal subtypes in the cerebral cortex and axonal guidance in the floor plate.; ","epilepsy",{"$nulls":3},"p.Gly397fs","c.1187dupC","HIGH","396/562",4,{"$nulls":5},"5","192","135","145","95","137","100","0","0","0","0.11",{"$nulls":5},"(ARX|ENSG00000004848|1|1.00)",{"$nulls":25},"Unknown",-1,"XL","Partington X-linked mental retardation syndrome; Epileptic encephalopathy, early infantile, 1; Lissencephaly, X-linked 2; Hydranencephaly with abnormal genitalia; Mental retardation, X-linked 29/32/33/38/43/54/76/87; Proud syndrome; Corpus callosum, agenesis of, with abnormal genitalia","Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic",null,"This gene is a homeobox-containing gene expressed during development. The expressed protein contains two conserved domains, a C-peptide (or aristaless domain) and the prd-like class homeobox domain. It is a member of the group-II aristaless-related protein family whose members are expressed primarily in the central and/or peripheral nervous system. This gene is thought to be involved in CNS development. Mutations in this gene cause X-linked mental retardation and epilepsy. [provided by RefSeq, Jul 2008].  ",null,"C3463992| C0796250| C0796124| C1846171| C0796244","0/0","171,0","0","171","0/1","109,12","0.0992","121",null,"chrX:25007371:A:AG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0737"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","BABAM1","chr19:17269071","BABAM1(V89I)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the BRCA1-A complex, a complex that specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). The BRCA1-A complex also possesses deubiquitinase activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. In the BRCA1-A complex, it is required for the complex integrity and its localization at DSBs. Component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys- 63'-linked ubiquitin in various substrates (PubMed:24075985, PubMed:26195665). In these 2 complexes, it is probably required to maintain the stability of BABAM2 and help the 'Lys-63'-linked deubiquitinase activity mediated by BRCC3/BRCC36 component. The BRISC complex is required for normal mitotic spindle assembly and microtubule attachment to kinetochores via its role in deubiquitinating NUMA1 (PubMed:26195665). Plays a role in interferon signaling via its role in the deubiquitination of the interferon receptor IFNAR1; deubiquitination increases IFNAR1 activity by enhancing its stability and cell surface expression (PubMed:24075985). Down-regulates the response to bacterial lipopolysaccharide (LPS) via its role in IFNAR1 deubiquitination (PubMed:24075985). {ECO:0000269|PubMed:19261746, ECO:0000269|PubMed:19261748, ECO:0000269|PubMed:19261749}.; ",{"$nulls":4},"p.Val89Ile","c.265G>A","MODERATE","89/329",2,{"$nulls":5},"5","252","251","183","174","213","209","0","0","0","0.0957",{"$nulls":20},"3.92248",null,"1.995;.;1.995;.;.;1.995;.;.;.;.;.","0.999417",".;-0.38;-0.38;.;.;.;.;.;.;.;.","0.8;.;0.8;.;.;0.8;.;.;.;.;.",".;0.124;0.114;.;.;.;.;.;.;.;.","0.377;0.449;0.377;.;.;0.378;.;.;0.443;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","248,0","0","248","0/1","214,27","0.112","241",null,"chr19:17269071:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1264"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","BCAN","chr1:156652398","BCAN(P483L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the terminally differentiating and the adult nervous system during postnatal development. Could stabilize interactions between hyaluronan (HA) and brain proteoglycans.; ",{"$nulls":4},"p.Pro483Leu","c.1448C>T","MODERATE","483/911",8,{"$nulls":5},"5","187","207","150","175","144","165","0","0","0","0.1576",{"$nulls":20},"1.73867","2.56;3.25","1.61","0.949173","-3.1;-2.81","0.0;0.001","0.001","0.235;0.115",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","187,0","0","187","0/1","173,33","0.1602","206",null,"chr1:156652398:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1543"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","BCL9","chr1:147624661","BCL9(G1328E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in signal transduction through the Wnt pathway. Promotes beta-catenin's transcriptional activity (By similarity). {ECO:0000250, ECO:0000269|PubMed:11955446}.; ","gedi|level2",{"$nulls":3},"p.Gly1328Glu","c.3983G>A","MODERATE","1328/1426",10,{"$nulls":5},"5","837","820","633","633","729","692","0","0","0","0.1734",{"$nulls":20},"3.310992","-0.13","2.045","0.999995","-1.92","0.306",null,"0.906",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","811,0","0","811","0/1","649,138","0.1753","787",null,"chr1:147624661:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1801"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CABIN1","chr22:24095991","CABIN1(G1283S)",{"$nulls":6},255,"PASS","Missense","rs894841298",-1,null,"FUNCTION: May be required for replication-independent chromatin assembly. May serve as a negative regulator of T-cell receptor (TCR) signaling via inhibition of calcineurin. Inhibition of activated calcineurin is dependent on both PKC and calcium signals. Acts as a negative regulator of p53/TP53 by keeping p53 in an inactive state on chromatin at promoters of a subset of it's target genes. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:9655484}.; ",{"$nulls":4},"p.Gly1283Ser","c.3847G>A","MODERATE","1283/2220",25,{"$nulls":5},"4","657","534","455","361","624","493","0","0","0","0.14",{"$nulls":20},"1.363774","0.29;.;0.08;0.29","-0.345;.;.;-0.345","0.995457","0.73;.;0.76;0.73","0.0;.;.;0.0","0.762;.;0.755;0.762","0.149;0.186;0.176;0.124",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","640,0","0","640","0/1","427,72","0.1443","499",null,"chr22:24095991:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.144"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CAPN9","chr1:230779116","CAPN9(G366D)",null,null,"region of interest (Domain III )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium-regulated non-lysosomal thiol-protease.; ",{"$nulls":4},"p.Gly366Asp","c.1097G>A","MODERATE","366/690",9,{"$nulls":5},"5","217","230","153","169","206","213","0","0","0","0.2441",{"$nulls":20},"4.12849","-5.85","4.12;.;.","1","-6.76","1.0","0.0","0.89;0.884;0.887",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is expressed predominantly in stomach and small intestine and may have specialized functions in the digestive tract. This gene is thought to be associated with gastric cancer. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].",null,null,"0/0","214,0","0","214","0/1","160,59","0.2694","219",null,"chr1:230779116:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2485"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CHEK1","chr11:125644111","CHEK1(S331F)",null,null,"modified residue (Phosphoserine )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle arrest and activation of DNA repair in response to the presence of DNA damage or unreplicated DNA. May also negatively regulate cell cycle progression during unperturbed cell cycles. This regulation is achieved by a number of mechanisms that together help to preserve the integrity of the genome. Recognizes the substrate consensus sequence [R-X-X-S/T]. Binds to and phosphorylates CDC25A, CDC25B and CDC25C. Phosphorylation of CDC25A at 'Ser-178' and 'Thr-507' and phosphorylation of CDC25C at 'Ser-216' creates binding sites for 14-3-3 proteins which inhibit CDC25A and CDC25C. Phosphorylation of CDC25A at 'Ser-76', 'Ser- 124', 'Ser-178', 'Ser-279' and 'Ser-293' promotes proteolysis of CDC25A. Phosphorylation of CDC25A at 'Ser-76' primes the protein for subsequent phosphorylation at 'Ser-79', 'Ser-82' and 'Ser-88' by NEK11, which is required for polyubiquitination and degradation of CDCD25A. Inhibition of CDC25 leads to increased inhibitory tyrosine phosphorylation of CDK-cyclin complexes and blocks cell cycle progression. Also phosphorylates NEK6. Binds to and phosphorylates RAD51 at 'Thr-309', which promotes the release of RAD51 from BRCA2 and enhances the association of RAD51 with chromatin, thereby promoting DNA repair by homologous recombination. Phosphorylates multiple sites within the C-terminus of TP53, which promotes activation of TP53 by acetylation and promotes cell cycle arrest and suppression of cellular proliferation. Also promotes repair of DNA cross-links through phosphorylation of FANCE. Binds to and phosphorylates TLK1 at 'Ser-743', which prevents the TLK1-dependent phosphorylation of the chromatin assembly factor ASF1A. This may enhance chromatin assembly both in the presence or absence of DNA damage. May also play a role in replication fork maintenance through regulation of PCNA. May regulate the transcription of genes that regulate cell- cycle progression through the phosphorylation of histones. Phosphorylates histone H3.1 (to form H3T11ph), which leads to epigenetic inhibition of a subset of genes. May also phosphorylate RB1 to promote its interaction with the E2F family of transcription factors and subsequent cell cycle arrest.; ","gedi|foundationOne|level2","[ \"Dacarbazine\" , \"Paclitaxel\" , \"Temozolomide\"]","[ \"Dacarbazine\" , \"Paclitaxel\" , \"Temozolomide\"]","[ \"Dacarbazine\" , \"Paclitaxel\" , \"Temozolomide\"]","p.Ser331Phe","c.992C>T","MODERATE","331/492",9,{"$nulls":5},"5","313","210","274","195","240","159","0","0","0","0.1698",{"$nulls":20},"3.945156",".;1.81;1.81;1.81;.;1.81;1.81;1.81","2.82;2.82;.;2.82;.;2.82;2.82;.","1",".;-3.07;-2.76;-3.07;.;-3.07;-3.07;-3.05",".;0.942;0.942;0.942;.;0.942;0.942;.",".;0.013;0.002;0.013;.;0.013;0.013;0.011","0.837;0.802;0.729;0.802;0.806;0.802;0.805;0.732",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE,kP53",{"$nulls":3},"0/0","310,0","0","310","0/1","182,31","0.1455","213",null,"chr11:125644111:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1436"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CHL1","chr3:389396","CHL1(D798N)",null,null,"topological domain (Extracellular ), domain (Fibronectin type-III 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Extracellular matrix and cell adhesion protein that plays a role in nervous system development and in synaptic plasticity. Both soluble and membranous forms promote neurite outgrowth of cerebellar and hippocampal neurons and suppress neuronal cell death. Plays a role in neuronal positioning of pyramidal neurons and in regulation of both the number of interneurons and the efficacy of GABAergic synapses. May play a role in regulating cell migration in nerve regeneration and cortical development. Potentiates integrin-dependent cell migration towards extracellular matrix proteins. Recruits ANK3 to the plasma membrane (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp798Asn","c.2392G>A","MODERATE","798/1224",20,1,{"$nulls":4},"5","531","322","367","234","481","296","0","0","0","0.2162",{"$nulls":20},"3.999936","0.54;0.54;.",null,"0.998501","-2.0;-2.1;.","0.944;0.541;.","0.035;0.033;.","0.42;0.426;0.453",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","512,0","0","512","0/1","235,64","0.214","299",null,"chr3:389396:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2137"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CLVS1","chr8:61299921","CLVS1(P32S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). {ECO:0000250, ECO:0000269|PubMed:19651769}.; ",{"$nulls":4},"p.Pro32Ser","c.94C>T","MODERATE","32/354",2,{"$nulls":5},"5","434","386","357","326","344","337","0","0","0","0.178",{"$nulls":20},"1.906094",".;-1.33;-1.33",".;1.425;1.425","0.999948;0.999948;1","-4.12;-1.67;-1.67","0.256;0.258;0.258","0.123;0.173;0.173",".;0.227;0.228",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","431,0","0","431","0/1","315,62","0.1645","377",null,"chr8:61299921:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1687"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CNGB1","chr16:57919188","CNGB1(E623G)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform RCNC2A. ), splice variant (In isoform GARP2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Retinitis pigmentosa 45 (RP45) [MIM:613767]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:11379879}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Subunit of cyclic nucleotide-gated (CNG) channels, nonselective cation channels, which play important roles in both visual and olfactory signal transduction. When associated with CNGA1, it is involved in the regulation of ion flow into the rod photoreceptor outer segment (ROS), in response to light-induced alteration of the levels of intracellular cGMP.; ",{"$nulls":4},"p.Glu623Gly","c.1868A>G","MODERATE","623/1251",20,{"$nulls":5},"4","717","563","487","375","678","525","0","0","0","0.1238",{"$nulls":20},"3.190448","-1.19","1.56;.","0.999969","-5.45","0.013;.","0.004","0.309;0.287",{"$nulls":3},"Unknown",-1,"AR","Retinitis pigmentosa 45","Ophthalmologic",{"$nulls":3},"C3151066","0/0","709,0","0","709","0/1","483,70","0.1266","553",null,"chr16:57919188:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1173"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","CREBBP","chr16:3773828","CREBBP(Q796*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Chromosomal aberrations involving CREBBP may be a cause of acute myeloid leukemias. Translocation t(8;16)(p11;p13) with KAT6A; translocation t(11;16)(q23;p13.3) with KMT2A/MLL1; translocation t(10;16)(q22;p13) with KAT6B. KAT6A-CREBBP may induce leukemia by inhibiting RUNX1-mediated transcription.; DISEASE: Rubinstein-Taybi syndrome 1 (RSTS1) [MIM:180849]: A disorder characterized by craniofacial abnormalities, postnatal growth deficiency, broad thumbs, broad big toes, mental retardation and a propensity for development of malignancies. {ECO:0000269|PubMed:11331617, ECO:0000269|PubMed:12114483, ECO:0000269|PubMed:12566391, ECO:0000269|PubMed:15706485, ECO:0000269|PubMed:20684013, ECO:0000269|PubMed:24616510, ECO:0000269|PubMed:25388907}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=De novo missense mutations in the last part of exon 30 or beginning of exon 31 are associated with growth retardation, craniofacial dysmorphism and additional Rubinstein-Taybi-like features. No patients have broad thumbs. Patients have intellectual disability of variable severity, a marked speech delay, short stature and microcephaly. Main facial characteristics include short palpebral fissures, telecanthi, depressed nasal ridge, short nose, anteverted nares, short columella and long philtrum. {ECO:0000269|PubMed:27311832}.; ","FUNCTION: Acetylates histones, giving a specific tag for transcriptional activation. Also acetylates non-histone proteins, like NCOA3 and FOXO1. Binds specifically to phosphorylated CREB and enhances its transcriptional activity toward cAMP-responsive genes. Acts as a coactivator of ALX1. Acts as a circadian transcriptional coactivator which enhances the activity of the circadian transcriptional activators: NPAS2-ARNTL/BMAL1 and CLOCK- ARNTL/BMAL1 heterodimers. Acetylates PCNA; acetylation promotes removal of chromatin-bound PCNA and its degradation during nucleotide excision repair (NER) (PubMed:24939902). Functions as a transcriptional coactivator for SMAD4 in the TGF-beta signaling pathway (PubMed:25514493). {ECO:0000269|PubMed:11154691, ECO:0000269|PubMed:12738767, ECO:0000269|PubMed:12929931, ECO:0000269|PubMed:14645221, ECO:0000269|PubMed:24939902, ECO:0000269|PubMed:25514493, ECO:0000269|PubMed:9707565}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Gln796*","c.2386C>T","HIGH","796/2442",13,{"$nulls":5},"4","632","478","469","364","528","402","0","0","0","0.2587",{"$nulls":5},"(CREBBP|ENSG00000005339|1|1.00)","(CREBBP|ENSG00000005339|1|1.00)",{"$nulls":13},"7.603001",null,null,"1",{"$nulls":3},"0.95;0.946;.",{"$nulls":3},"Unknown",-1,"AD","Rubinstein-Taybi syndrome","Allergy/Immunology/Infectious; Cardiovascular; Craniofacial; Musculoskeletal; Neurologic ; Oncologic; Ophthalmologic","COSMIC,kCANCER,kCELL_CYCLE,kJAK_STAT,kNOTCH,kTGF_BETA,kWNT",null,null,"C5193034| C4551859","0/0","616,0","0","616","0/1","357,115","0.2436","472",null,"chr16:3773828:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2473"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","DBNL","chr7:44057782","DBNL(G159S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Adapter protein that binds F-actin and DNM1, and thereby plays a role in receptor-mediated endocytosis. Plays a role in the reorganization of the actin cytoskeleton, formation of cell projections, such as neurites, in neuron morphogenesis and synapse formation via its interaction with WASL and COBL. Does not bind G- actin and promote actin polymerization by itself. Required for the formation of organized podosome rosettes (By similarity). May act as a common effector of antigen receptor-signaling pathways in leukocytes. Acts as a key component of the immunological synapse that regulates T-cell activation by bridging TCRs and the actin cytoskeleton to gene activation and endocytic processes. {ECO:0000250, ECO:0000269|PubMed:14729663}.; ",{"$nulls":4},"p.Gly159Ser","c.475G>A","MODERATE","159/439",6,{"$nulls":5},"5","392","278","315","236","321","231","0","0","0","0.2294",{"$nulls":20},"4.834661","1.57;1.16;1.08;1.35;1.24;0.84;1.43","3.305;.;.;.;.;3.305;3.305","1","-5.62;-5.72;-5.85;-5.69;-5.69;-5.62;-5.62","1.0;.;.;.;1.0;1.0;1.0","0.0","0.262;0.266;0.358;0.256;0.279;0.265;0.268",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","388,0","0","388","0/1","214,56","0.2074","270",null,"chr7:44057782:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2203"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","DDR2","chr1:162755230","DDR2(V164V)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs1329164508",-1,"DISEASE: Spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:271665]: A bone disease characterized by short- limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping. {ECO:0000269|PubMed:19110212, ECO:0000269|PubMed:20223752, ECO:0000269|PubMed:26463668}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation, remodeling of the extracellular matrix, cell migration and cell proliferation. Required for normal bone development. Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing. {ECO:0000269|PubMed:16186104, ECO:0000269|PubMed:16186108, ECO:0000269|PubMed:17665456, ECO:0000269|PubMed:18201965, ECO:0000269|PubMed:20004161, ECO:0000269|PubMed:20564243, ECO:0000269|PubMed:20734453, ECO:0000269|PubMed:9659899}.; ","gedi|foundationOne","[ \"Dasatinib\"]","[ \"Dasatinib\"]","[ \"Dasatinib\"]",null,"c.492C>T","HIGH",null,6,{"$nulls":5},"4","354","370","228","251","325","319","0","0","0","0.2414",{"$nulls":31},"Unknown",-1,"AR","Spondylometaepiphyseal dysplasia, short limb-hand type","Craniofacial; Musculoskeletal",{"$nulls":3},"C5193019| C1849011","0/0","346,0","0","346","0/1","263,100","0.2755","363",null,"chr1:162755230:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2829"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","DDX43","chr6:73407606","DDX43(G343E)",null,null,"domain (Helicase ATP-binding ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs574167373",0.000992063492063492,{"$nulls":6},"p.Gly343Glu","c.1028G>A","MODERATE","343/648",8,{"$nulls":5},"5","342","233","219","155","322","219","0","0","0","0.21",{"$nulls":20},"2.799121","3.36","1.8","0.999679;1","-4.79","0.898","0.005","0.54",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":7},"0/0","337,0","0","337","0/1","177,49","0.2168","226",null,"chr6:73407606:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2065"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","DNAJC30","chr7:73682814","DNAJC30(E204K)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu204Lys","c.610G>A","MODERATE","204/226",1,2,{"$nulls":4},"5","860","746","666","561","764","645","0","0","0","0.0884",{"$nulls":20},"2.358359","0.42","1.355","0.926306","-1.11","0.454","0.328","0.047",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","820,0","0","820","0/1","659,62","0.086","721",null,"chr7:73682814:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0856"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","DNHD1","chr11:6538428","DNHD1(I1015T)",null,null,"splice variant (In isoform 2 and isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ile1015Thr","c.3044T>C","MODERATE","1015/4753",15,{"$nulls":5},"4","534","407","441","343","401","314","0","0","0","0.121",{"$nulls":20},"3.656065","-0.01","1.1","0.991588","-2.21","1.0","0.007","0.742;0.764",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","526,0","0","526","0/1","353,39","0.0995","392",null,"chr11:6538428:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0991"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","EGR3","chr8:22690861","EGR3(R259fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Probable transcription factor involved in muscle spindle development.; ",{"$nulls":4},"p.Arg259fs","c.775delC","HIGH","259/387",2,{"$nulls":5},"5","512","592","432","505","429","515","0","0","0","0.1165",{"$nulls":5},"(EGR3|ENSG00000179388|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","491,0","0","491","0/1","483,69","0.125","552",null,"chr8:22690861:CG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1149"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ENAM","chr4:70644472","ENAM(P1016S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Amelogenesis imperfecta 1B (AI1B) [MIM:104500]: An autosomal dominant defect of enamel formation. Clinical manifestations may be variable. Some cases present with generalized enamel hypoplasia resulting in small, smooth, yellow and widely spaced teeth (smooth hypoplastic AI). Others show horizontal rows of pits, grooves or a hypoplastic area in the enamel (local hypoplastic AI). {ECO:0000269|PubMed:11487571, ECO:0000269|PubMed:11978766, ECO:0000269|PubMed:20439930, ECO:0000269|PubMed:25789606}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Amelogenesis imperfecta 1C (AI1C) [MIM:204650]: An autosomal recessive defect of dental enamel formation. Teeth show local hypoplastic and unmineralized enamel, and a yellow-brown discoloration. Enamel defects can be associated with facial and oral features including vertical dysgnathia and anterior openbite malocclusion. {ECO:0000269|PubMed:14684688, ECO:0000269|PubMed:20439930, ECO:0000269|PubMed:25789606}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the mineralization and structural organization of enamel. Involved in the extension of enamel during the secretory stage of dental enamel formation. {ECO:0000250|UniProtKB:O97939}.; ",{"$nulls":4},"p.Pro1016Ser","c.3046C>T","MODERATE","1016/1142",9,{"$nulls":5},"5","676","474","529","372","573","418","0","0","0","0.2033",{"$nulls":20},"3.349668","0.57","3.465","0.977542","-7.83","1.0","0.002","0.693",{"$nulls":3},"Unknown",-1,"AR","Amelogenesis imperfecta, type IB; Amelogenesis imperfecta, type IC","Dental ",{"$nulls":3},"C0399368| C2673923","0/0","667,0","0","667","0/1","373,96","0.2047","469",null,"chr4:70644472:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2043"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ESCO2","chr8:27776883","ESCO2(P192L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Roberts syndrome (RBS) [MIM:268300]: Rare autosomal recessive disorder characterized by pre- and postnatal growth retardation, microcephaly, bilateral cleft lip and palate, and mesomelic symmetric limb reduction. Severely affected infants may be stillborn or die shortly after birth. RBS chromosomes have a lack of cohesion involving the heterochromatic C-banding regions around centromeres and the distal portion of the long arm of the Y chromosome (known as premature centromere separation, heterochromatin repulsion or puffing, or RS effect). {ECO:0000269|PubMed:15821733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: SC phocomelia syndrome (SCPS) [MIM:269000]: Has a milder phenotype than RBS, with a lesser degree of symmetric limb reduction and additionally includes flexion contractures of various joints, midfacial hemangioma, hypoplastic cartilage of ears and nose, scant silvery-blond hair, and cloudy corneae. Although microcephaly is present, mental retardation may be mild and survival into adulthood is common. {ECO:0000269|PubMed:16380922}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acetyltransferase required for the establishment of sister chromatid cohesion (PubMed:15821733, PubMed:15958495). Couples the processes of cohesion and DNA replication to ensure that only sister chromatids become paired together. In contrast to the structural cohesins, the deposition and establishment factors are required only during the S phase. Acetylates the cohesin component SMC3 (PubMed:21111234). {ECO:0000269|PubMed:15821733, ECO:0000269|PubMed:15958495, ECO:0000269|PubMed:19907496, ECO:0000269|PubMed:21111234}.; ",{"$nulls":4},"p.Pro192Leu","c.575C>T","MODERATE","192/601",3,{"$nulls":5},"5","655","600","510","469","579","502","0","0","0","0.0777",{"$nulls":20},"2.562131","-0.11","2.52","0.978483;1","-3.16","0.986","0.018","0.439",{"$nulls":3},"Unknown",-1,"AR","SC phocomelia syndrome; Roberts syndrome","Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic",{"$nulls":3},"C0392475| C0392475","0/0","651,0","0","651","0/1","538,44","0.0756","582",null,"chr8:27776883:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0682"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","FAM83E","chr19:48603786","FAM83E(P295L)",{"$nulls":6},255,"PASS","Missense","rs540259397",-1,null,"FUNCTION: May play a role in MAPK signaling. {ECO:0000303|PubMed:24736947}.; ",{"$nulls":4},"p.Pro295Leu","c.884C>T","MODERATE","295/478",4,{"$nulls":5},"5","379","325","279","243","317","277","0","0","0","0.1949",{"$nulls":20},"3.182594","2.03","2.24","1","-1.07","0.997","0.023","0.316",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","365,0","0","365","0/1","239,62","0.206","301",null,"chr19:48603786:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2058"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","FBXO34","chr14:55351913","FBXO34(A508V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate-recognition component of the SCF (SKP1-CUL1-F- box protein)-type E3 ubiquitin ligase complex. {ECO:0000250}.; ",{"$nulls":4},"p.Ala508Val","c.1523C>T","MODERATE","508/711",2,{"$nulls":5},"4","484","375","394","307","422","332","0","0","0","0.1054",{"$nulls":20},"0.77088","2.24","1.95","1","-0.31","0.328","0.119","0.026;0.033",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","481,0","0","481","0/1","334,38","0.1022","372",null,"chr14:55351913:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1042"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","FOCAD","chr9:20926394","FOCAD(Q1019*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Potential tumor suppressor in gliomas. {ECO:0000250, ECO:0000269|PubMed:22427331}.; ",{"$nulls":4},"p.Gln1019*","c.3055C>T","HIGH","1019/1801",25,{"$nulls":5},"5","505","421","333","287","478","386","0","0","0","0.1839",{"$nulls":5},"(FOCAD|ENSG00000188352|1|1.00)","(FOCAD|ENSG00000188352|1|1.00)",{"$nulls":13},"8.335155",null,null,"1",{"$nulls":3},"0.36;0.36;0.364",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","502,0","0","502","0/1","325,80","0.1975","405",null,"chr9:20926394:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1812"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","FPR3","chr19:51824461","FPR3(R238H)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs764805147",6.064e-05,null,"FUNCTION: Low affinity receptor for N-formyl-methionyl peptides, which are powerful neutrophils chemotactic factors. Binding of FMLP to the receptor causes activation of neutrophils. This response is mediated via a G-protein that activates a phosphatidylinositol-calcium second messenger system.; ",{"$nulls":4},"p.Arg238His","c.713G>A","MODERATE","238/353",2,4,{"$nulls":4},"5","694","539","542","427","606","473","0","0","0","0.1945",{"$nulls":20},"0.640544","0.94","2.385","0.999179","-3.62;.","0.493","0.028;.","0.148;0.144",{"$nulls":3},"ExAC_SAS_AF",6.064e-05,{"$nulls":7},"0/0","680,0","0","680","0/1","428,109","0.203","537",null,"chr19:51824461:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2037"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","FSD1","chr19:4317215","FSD1(R245H)",null,null,"domain (Fibronectin type-III )",{"$nulls":3},255,"PASS","Missense","rs765462502",9.6140000000000011E-5,null,"FUNCTION: May be involved in microtubule organization and stabilization. {ECO:0000269|PubMed:12154070, ECO:0000269|PubMed:12445389}.; ",{"$nulls":4},"p.Arg245His","c.734G>A","MODERATE","245/496",8,1,{"$nulls":4},"5","413","326","285","235","374","277","0","0","0","0.0975",{"$nulls":20},"4.320314","0.69","3.725;.","0.999994","-2.49;.","1.0;.","0.023;.","0.926;0.956",{"$nulls":3},"ExAC_AFR_AF",9.6140000000000011E-5,{"$nulls":7},"0/0","405,0","0","405","0/1","285,32","0.1009","317",null,"chr19:4317215:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0979"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","GGA2","chr16:23480677","GGA2(T325I)",null,null,"region of interest (Unstructured hinge )","modified-residue:phosphothreonine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF- dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (AC-LL) motif.; ",{"$nulls":4},"p.Thr325Ile","c.974C>T","MODERATE","325/613",10,{"$nulls":5},"5","491","348","370","257","432","296","0","0","0","0.2297",{"$nulls":20},"1.893357","2.52","1.175","1;0.999992","-1.58","0.015","0.044","0.145",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","480,0","0","480","0/1","256,80","0.2381","336",null,"chr16:23480677:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.249"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","GOLGA1","chr9:124890388","GOLGA1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss","rs768425423",1.499E-5,null,"FUNCTION: Involved in vesicular trafficking at the Golgi apparatus level. Involved in endosome-to-Golgi trafficking. {ECO:0000269|PubMed:29084197}.; ",{"$nulls":5},"c.1497+1G>A","HIGH",null,16,{"$nulls":5},"4","319","268","261","221","266","209","0","0","0","0.1531",{"$nulls":5},"(GOLGA1|ENSG00000136935|1|1.00)",{"$nulls":14},"5.133202",null,null,"1",{"$nulls":7},"ExAC_NFE_AF",1.499E-5,{"$nulls":7},"0/0","317,0","0","317","0/1","218,48","0.1805","266",null,"chr9:124890388:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1719"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","GOLGA2","chr9:128257491","GOLGA2(R891Q)",{"$nulls":6},255,"PASS","Missense","rs745789468",6.06e-05,null,"FUNCTION: Peripheral membrane component of the cis-Golgi stack that acts as a membrane skeleton that maintains the structure of the Golgi apparatus, and as a vesicle thether that facilitates vesicle fusion to the Golgi membrane (Probable) (PubMed:16489344). Required for normal protein transport from the endoplasmic reticulum to the Golgi apparatus and the cell membrane (By similarity). Together with p115/USO1 and STX5, involved in vesicle tethering and fusion at the cis-Golgi membrane to maintain the stacked and inter-connected structure of the Golgi apparatus. Plays a central role in mitotic Golgi disassembly: phosphorylation at Ser-37 by CDK1 at the onset of mitosis inhibits the interaction with p115/USO1, preventing tethering of COPI vesicles and thereby inhibiting transport through the Golgi apparatus during mitosis (By similarity). Also plays a key role in spindle pole assembly and centrosome organization (PubMed:26165940). Promotes the mitotic spindle pole assembly by activating the spindle assembly factor TPX2 to nucleate microtubules around the Golgi and capture them to couple mitotic membranes to the spindle: upon phosphorylation at the onset of mitosis, GOLGA2 interacts with importin-alpha via the nuclear localization signal region, leading to recruit importin-alpha to the Golgi membranes and liberate the spindle assembly factor TPX2 from importin-alpha. TPX2 then activates AURKA kinase and stimulates local microtubule nucleation. Upon filament assembly, nascent microtubules are further captured by GOLGA2, thus linking Golgi membranes to the spindle (PubMed:19242490, PubMed:26165940). Regulates the meiotic spindle pole assembly, probably via the same mechanism (By similarity). Also regulates the centrosome organization (PubMed:18045989, PubMed:19109421). Also required for the Golgi ribbon formation and glycosylation of membrane and secretory proteins (PubMed:16489344, PubMed:17314401). {ECO:0000250|UniProtKB:Q62839, ECO:0000250|UniProtKB:Q921M4, ECO:0000269|PubMed:16489344, ECO:0000269|PubMed:17314401, ECO:0000269|PubMed:18045989, ECO:0000269|PubMed:19109421, ECO:0000269|PubMed:19242490, ECO:0000269|PubMed:26165940, ECO:0000305|PubMed:26363069}.; ",{"$nulls":4},"p.Arg891Gln","c.2672G>A","MODERATE","891/1002",25,{"$nulls":5},"5","369","316","283","228","324","283","0","0","0","0.1166",{"$nulls":20},"1.449285","1.8;.;.;.","0.92;0.92;.;.","0.995112","-1.43;.;.;.","0.995;0.995;.;.","0.362;.;.;.","0.224;0.225;0.23;0.25",{"$nulls":3},"ExAC_SAS_AF",6.06e-05,{"$nulls":7},"0/0","366,0","0","366","0/1","274,35","0.1133","309",null,"chr9:128257491:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1228"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","GRHL3","chr1:24347506","GRHL3(D528fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcription factor playing important roles in primary neurulation and in the differentiation of stratified epithelia of both ectodermal and endodermal origin (By similarity). Binds directly to the consensus DNA sequence 5'-AACCGGTT-3' acting as an activator and repressor on distinct target genes (PubMed:21081122, PubMed:25347468). xhibits functional redundancy with GRHL2 in epidermal morphogenetic events and epidermal wound repair (By similarity). Exhibits functional redundancy with GRHL2 in epidermal morphogenetic events and epidermal wound repair but is essential to form the epidermal barrier with TGM3 as critical direct target gene among others. Despite being dispensable during normal epidermal homeostasis in the adulthood, is again required for barrier repair after immune-mediated epidermal damage, regulates distinct gene batteries in embryonic epidermal differentiation and adult epidermal barrier reformation after injury. Plays unique and cooperative roles with GRHL2 in establishing distinct zones of primary neurulation. Essential for spinal closure, functions cooperatively with GRHL2 in closure 2 (forebrain/midbrain boundary) and posterior neuropore closure (By similarity). Also required for proper development of the oral periderm (PubMed:24360809). No genetic interaction with GRHL3, no functional cooperativity due to diverse target gene selectivity (PubMed:21081122). {ECO:0000250|UniProtKB:Q5FWH3, ECO:0000269|PubMed:12549979, ECO:0000269|PubMed:21081122, ECO:0000269|PubMed:24360809, ECO:0000269|PubMed:25347468}.; ",{"$nulls":4},"p.Asp528fs","c.1583_1584delAC","HIGH","528/626",14,{"$nulls":5},"4","728","583","504","381","645","507","0","0","0","0.0947",{"$nulls":5},"(GRHL3|ENSG00000158055|1|1.00)",{"$nulls":25},"Unknown",-1,"AD","van der Woude syndrome 2","Craniofacial; Dental; Musculoskeletal",{"$nulls":3},"C1847604","0/0","695,0","0","695","0/1","482,55","0.1024","537",null,"chr1:24347506:GAC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1024"]
["09JM","T11","JLPIKTOR_JLPIKTOR_17113009JM","HMCN2","chr9:130424847","HMCN2(A4465T)",{"$nulls":6},255,"PASS","Missense","rs1368870698",-1,{"$nulls":6},"p.Ala4465Thr","c.13393G>A","MODERATE","4465/5059",88,{"$nulls":5},"4","1160","686","877","516","958","540","0","0","0","0.0593",{"$nulls":20},"3.111371",{"$nulls":6},"0.118",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1130,0","0","1130","0/1","624,38","0.0574","662",null,"chr9:130424847:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.062"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","HNRNPM","chr19:8486208","HNRNPM(P594S)",null,null,"region of interest (27 X 6 AA repeats of [GEVSTPAN]-[ILMV]-[DE]-[RH]-[MLVI]-[GAV] )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines.; ",{"$nulls":4},"p.Pro594Ser","c.1780C>T","MODERATE","594/730",14,{"$nulls":5},"3","1057","874",null,null,"493","438","0","0","0","0.2374",{"$nulls":20},"2.210545","2.87;2.51;.",".;1.67;.","0.999388;0.999547","-1.48;-1.59;.","1.0;0.259;.","0.111;0.157;.","0.203;0.173;0.177",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1023,0","0","1023","0/1","654,214","0.2465","868",null,"chr19:8486208:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","INPP5J","chr22:31134339","INPP5J(R981W)",{"$nulls":6},255,"PASS","Missense","rs185902428",9.9403578528827028E-4,null,"FUNCTION: Inositol 5-phosphatase, which converts inositol 1,4,5- trisphosphate to inositol 1,4-bisphosphate. Also converts phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 4- phosphate and inositol 1,3,4,5-tetrakisphosphate to inositol 1,3,4-trisphosphate in vitro. May be involved in modulation of the function of inositol and phosphatidylinositol polyphosphate- binding proteins that are present at membranes ruffles (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg981Trp","c.2941C>T","MODERATE","981/1006",13,{"$nulls":5},"5","628","493","446","328","574","446","0","0","0","0.1211",{"$nulls":20},"2.666146",".;-4.49;-4.5;-5.05;-5.05;-5.05;-4.95;-3.94;-3.94",".;.;1.79;.;.;.;.;.;.","0.999615;0.999498;0.999498;0.999498;0.999904;0.999743;0.999743;0.999743",".;-1.37;-1.39;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37",".;.;0.991;0.968;0.968;0.894;0.83;.;.",".;0.001;0.001;0.004;0.004;0.005;0.001;0.001;0.001","0.174;0.161;0.184;0.18;0.18;0.157;0.188;0.149;0.147",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,{"$nulls":7},"0/0","616,0","0","616","0/1","422,59","0.1227","481",null,"chr22:31134339:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1098"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","IPO7","chr11:9438105","IPO7(L839F)",{"$nulls":6},255,"PASS","Missense","rs1300272724",-1,null,"FUNCTION: Functions in nuclear protein import, either by acting as autonomous nuclear transport receptor or as an adapter-like protein in association with the importin-beta subunit KPNB1. Acting autonomously, is thought to serve itself as receptor for nuclear localization signals (NLS) and to promote translocation of import substrates through the nuclear pore complex (NPC) by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Mediates autonomously the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. Binds to a beta-like import receptor binding (BIB) domain of RPL23A. In association with KPNB1 mediates the nuclear import of H1 histone and the Ran-binding site of IPO7 is not required but synergizes with that of KPNB1 in importin/substrate complex dissociation. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones. {ECO:0000269|PubMed:10228156, ECO:0000269|PubMed:9687515}.; ","gedi",{"$nulls":3},"p.Leu839Phe","c.2515C>T","MODERATE","839/1038",22,{"$nulls":5},"4","684","468","463","309","211","167","0","0","0","0.2216",{"$nulls":20},"2.9612540000000003","-0.5","2.025","1","-2.62","0.955","0.205","0.768",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","531,0","0","531","0/1","269,76","0.2203","345",null,"chr11:9438105:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.233"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ITGB3BP","chr1:63510138","ITGB3BP(R17C)",null,null,"modified residue (Phosphoserine )",{"$nulls":3},255,"PASS","Missense","rs561845071",-1,null,"FUNCTION: Transcription coregulator that can have both coactivator and corepressor functions. Isoform 1, but not other isoforms, is involved in the coactivation of nuclear receptors for retinoid X (RXRs) and thyroid hormone (TRs) in a ligand-dependent fashion. In contrast, it does not coactivate nuclear receptors for retinoic acid, vitamin D, progesterone receptor, nor glucocorticoid. Acts as a coactivator for estrogen receptor alpha. Acts as a transcriptional corepressor via its interaction with the NFKB1 NF- kappa-B subunit, possibly by interfering with the transactivation domain of NFKB1. Induces apoptosis in breast cancer cells, but not in other cancer cells, via a caspase-2 mediated pathway that involves mitochondrial membrane permeabilization but does not require other caspases. May also act as an inhibitor of cyclin A- associated kinase. Also acts a component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression and chromosome segregation. May be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex. {ECO:0000269|PubMed:11713274, ECO:0000269|PubMed:12244126, ECO:0000269|PubMed:15082778, ECO:0000269|PubMed:15254226, ECO:0000269|PubMed:16622420}.; ",{"$nulls":4},"p.Arg17Cys","c.49C>T","MODERATE","17/216",2,{"$nulls":5},"4","212","179","135","117","189","168","0","0","0","0.0536",{"$nulls":20},"0.535345","1.0",null,"1","0.18","0.983","0.026","0.187",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","197,0","0","197","0/1","163,10","0.0578","173",null,"chr1:63510138:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0769"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","KIAA0100","chr17:28638551","KIAA0100(A441T)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in membrane trafficking. {ECO:0000250|UniProtKB:K7VLR4}.; ",{"$nulls":4},"p.Ala441Thr","c.1321G>A","MODERATE","441/2235",12,{"$nulls":5},"5","507","329","371","247","451","296","0","0","0","0.1993",{"$nulls":20},"3.820021","1.45;1.22;1.22","1.1;.;.","1","-1.03;-0.94;.","1.0;.;.","0.015;0.007;.","0.866;0.846;0.848",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","500,0","0","500","0/1","258,71","0.2158","329",null,"chr17:28638551:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2105"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","KIAA1147","chr7:141664197","KIAA1147(P383S)",{"$nulls":6},255,"PASS","Missense","rs746039460",2.743E-4,null,"FUNCTION: May play a role in neuritogenesis, as well as in neuronal recovery and/or restructuring in the hippocampus following transient cerebral ischemia. {ECO:0000250}.; ",{"$nulls":4},"p.Pro383Ser","c.1147C>T","MODERATE","383/455",8,{"$nulls":5},"5","488","372","368","273","400","300","0","0","0","0.1533",{"$nulls":20},"1.920814",null,null,"0.974415;0.904747","-0.06;-0.44",null,"1.0","0.083;0.111",{"$nulls":3},"ExAC_AFR_AF",2.743E-4,{"$nulls":7},"0/0","476,0","0","476","0/1","307,45","0.1278","352",null,"chr7:141664197:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1355"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","KMT2C","chr7:152180800","KMT2C(Q2354*)",null,null,"sequence variant (In KLEFS2. ), sequence variant (In KLEFS2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Kleefstra syndrome 2 (KLEFS2) [MIM:617768]: A form of Kleefstra syndrome, an autosomal dominant disease characterized by variable mental retardation, psychomotor developmental delay, seizures, behavioral abnormalities, and facial dysmorphisms. {ECO:0000269|PubMed:22726846, ECO:0000269|PubMed:29069077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Histone methyltransferase. Methylates 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Central component of the MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. KMT2C/MLL3 may be a catalytic subunit of this complex. May be involved in leukemogenesis and developmental disorder. {ECO:0000269|PubMed:17500065}.; ",{"$nulls":4},"p.Gln2354*","c.7060C>T","HIGH","2354/4911",36,1,{"$nulls":4},"5","316","228","254","191","268","193","0","0","0","0.1917",{"$nulls":5},"(KMT2C|ENSG00000055609|1|1.00)","(KMT2C|ENSG00000055609|1|1.00)",{"$nulls":13},"7.746162",null,null,"1",{"$nulls":3},"0.916;0.907",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the myeloid/lymphoid or mixed-lineage leukemia (MLL) family and encodes a nuclear protein with an AT hook DNA-binding domain, a DHHC-type zinc finger, six PHD-type zinc fingers, a SET domain, a post-SET domain and a RING-type zinc finger. This protein is a member of the ASC-2/NCOA6 complex (ASCOM), which possesses histone methylation activity and is involved in transcriptional coactivation. [provided by RefSeq, Jul 2008].  ",null,"C4540395","0/0","319,0","0","319","0/1","184,43","0.1894","227",null,"chr7:152180800:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1832"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","KMT2D","chr12:49038988","KMT2D(Q2790*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Kabuki syndrome 1 (KABUK1) [MIM:147920]: A congenital mental retardation syndrome with additional features, including postnatal dwarfism, a peculiar facies characterized by long palpebral fissures with eversion of the lateral third of the lower eyelids, a broad and depressed nasal tip, large prominent earlobes, a cleft or high-arched palate, scoliosis, short fifth finger, persistence of fingerpads, radiographic abnormalities of the vertebrae, hands, and hip joints, and recurrent otitis media in infancy. {ECO:0000269|PubMed:20711175, ECO:0000269|PubMed:21280141, ECO:0000269|PubMed:21607748, ECO:0000269|PubMed:21658225, ECO:0000269|PubMed:21671394, ECO:0000269|PubMed:22126750, ECO:0000269|PubMed:23320472, ECO:0000269|PubMed:23913813, ECO:0000269|PubMed:24739679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Histone methyltransferase. Methylates 'Lys-4' of histone H3 (H3K4me). H3K4me represents a specific tag for epigenetic transcriptional activation. Acts as a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. {ECO:0000269|PubMed:16603732, ECO:0000269|PubMed:17500065, ECO:0000269|PubMed:17851529}.; ",{"$nulls":4},"p.Gln2790*","c.8368C>T","HIGH","2790/5537",34,{"$nulls":5},"3","255","185",{"$nulls":4},"0.0039","0.0039",{"$nulls":7},"(KMT2D|ENSG00000167548|1|1.00)","(KMT2D|ENSG00000167548|1|1.00)",{"$nulls":13},"7.733909",null,null,"1",{"$nulls":3},"0.903",{"$nulls":3},"Unknown",-1,"AD","Kabuki syndrome 1","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dental; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal",null,"The protein encoded by this gene is a histone methyltransferase that methylates the Lys-4 position of histone H3. The encoded protein is part of a large protein complex called ASCOM, which has been shown to be a transcriptional regulator of the beta-globin and estrogen receptor genes. Mutations in this gene have been shown to be a cause of Kabuki syndrome. [provided by RefSeq, Oct 2010].  CCDS Note: The full-length exon combination of this CCDS representation is inferred. It is mostly supported by the mRNA AF010403.1, but with correction of a gap in exon 10-11, supported by the mRNA AF010404.1, and by EST, RNA-Seq and orthologous transcript alignments.  ",null,"CN030661","0/0","252,1","0.004","253","0/1","138,53","0.2775","191",null,"chr12:49038988:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","LCE2A","chr1:152699143","LCE2A(R81Q)",null,null,"compositionally biased region (Cys-rich )",{"$nulls":3},255,"PASS","Missense","rs753692865",0.0001513,null,"FUNCTION: Precursors of the cornified envelope of the stratum corneum.; ",{"$nulls":4},"p.Arg81Gln","c.242G>A","MODERATE","81/106",2,2,{"$nulls":4},"5","619","692","482","527","407","495","0","0","0","0.2303",{"$nulls":20},"0.545082","3.76","1.6","0.999987","-0.5","0.216","0.092","0.111",{"$nulls":3},"ExAC_FIN_AF",0.0001513,{"$nulls":7},"0/0","606,0","0","606","0/1","520,147","0.2204","667",null,"chr1:152699143:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2315"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","LIFR","chr5:38505989","LIFR(Q403*)",{"$nulls":6},255,"PASS","Loss Of Function","rs145303192",1.1665888940737284E-4,"DISEASE: Stueve-Wiedemann syndrome (STWS) [MIM:601559]: Severe autosomal recessive condition and belongs to the group of the bent-bone dysplasias. SWS is characterized by bowing of the lower limbs, with internal cortical thickening, wide metaphyses with abnormal trabecular pattern, and camptodactyly. Additional features include feeding and swallowing difficulties, as well as respiratory distress and hyperthermic episodes, which cause death in the first months of life. The rare survivors develop progressive scoliosis, spontaneous fractures, bowing of the lower limbs, with prominent joints and dysautonomia symptoms, including temperature instability, absent corneal and patellar reflexes, and smooth tongue. {ECO:0000269|PubMed:14740318}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving LIFR is found in salivary gland pleiomorphic adenomas, the most common benign epithelial tumors of the salivary gland. Translocation t(5;8)(p13;q12) with PLAG1.; ","FUNCTION: Signal-transducing molecule. May have a common pathway with IL6ST. The soluble form inhibits the biological activity of LIF by blocking its binding to receptors on target cells.; ","gedi|level2",{"$nulls":3},"p.Gln403*","c.1207C>T","HIGH","403/1097",9,{"$nulls":5},"5","54","39","36","25","48","33","0","0","0","0.0909",{"$nulls":5},"(LIFR|ENSG00000113594|1|1.00)","(LIFR|ENSG00000113594|1|1.00)",{"$nulls":13},"6.819327",null,null,"1",{"$nulls":3},"0.973",{"$nulls":3},"ESP6500_EA_AF",1.1665888940737284E-4,"AR","Stuve-Wiedemann syndrome","Musculoskeletal; Neurologic","COSMIC,kJAK_STAT",null,null,"C0796176","0/0","53,0","0","53","0/1","35,4","0.1026","39",null,"chr5:38505989:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.12"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","LNX2","chr13:27562502","LNX2(G379S)",null,null,"domain (PDZ 2 )",{"$nulls":3},255,"PASS","Missense","rs367873891",6.0570000000000005E-5,{"$nulls":6},"p.Gly379Ser","c.1135G>A","MODERATE","379/690",5,1,{"$nulls":4},"4","461","363","356","286","405","323","0","0","0","0.1022",{"$nulls":20},"3.630961","0.18;.","3.29","1","-5.95;.","1.0","0.0;.","0.943;.",{"$nulls":3},"ExAC_SAS_AF",6.0570000000000005E-5,{"$nulls":7},"0/0","456,0","0","456","0/1","316,35","0.0997","351",null,"chr13:27562502:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0979"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","LZTS2","chr10:101003600","LZTS2(G171fs)",null,null,"region of interest (Required for centrosomal localization )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Negative regulator of katanin-mediated microtubule severing and release from the centrosome. Required for central spindle formation and the completion of cytokinesis. May negatively regulate axonal outgrowth by preventing the formation of microtubule bundles that are necessary for transport within the elongating axon. Negative regulator of the Wnt signaling pathway. Represses beta-catenin-mediated transcriptional activation by promoting the nuclear exclusion of beta-catenin. {ECO:0000255|HAMAP-Rule:MF_03026, ECO:0000269|PubMed:17000760, ECO:0000269|PubMed:17351128, ECO:0000269|PubMed:17950943, ECO:0000269|PubMed:18490357}.; ",{"$nulls":4},"p.Gly171fs","c.511_512insTGGGCCACCG","HIGH","171/669",2,{"$nulls":5},"5","657","533","481","395","513","405","0","0","0","0.1012",{"$nulls":5},"(LZTS2|ENSG00000107816|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","549,0","0","549","0/1","370,59","0.1375","429",null,"chr10:101003600:C:CGGGCCACCGT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1266"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","MARCO","chr2:118974423","MARCO(G184E)",null,null,"topological domain (Extracellular ), domain (Collagen-like )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Pattern recognition receptor (PRR) which binds Gram- positive and Gram-negative bacteria (PubMed:9468508). Also plays a role in binding of unopsonized particles by alveolar macrophages (By similarity). Binds to the secretoglobin SCGB3A2 (PubMed:12847263). {ECO:0000250|UniProtKB:Q9WUB9, ECO:0000269|PubMed:12847263, ECO:0000269|PubMed:9468508}.; ",{"$nulls":4},"p.Gly184Glu","c.551G>A","MODERATE","184/520",5,{"$nulls":5},"5","437","351","317","247","386","292","0","0","0","0.0651",{"$nulls":20},"2.366882","-6.28","3.905","1","-5.7","0.983","0.003","0.479",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a member of the class A scavenger receptor family and is part of the innate antimicrobial immune system. The protein may bind both Gram-negative and Gram-positive bacteria via an extracellular, C-terminal, scavenger receptor cysteine-rich (SRCR) domain. In addition to short cytoplasmic and transmembrane domains, there is an extracellular spacer domain and a long, extracellular collagenous domain. The protein may form a trimeric molecule by the association of the collagenous domains of three identical polypeptide chains. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","432,0","0","432","0/1","306,28","0.0838","334",null,"chr2:118974423:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0931"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","MEIS2","chr15:37093586","MEIS2(D212N)",null,null,"compositionally biased region (Ser/Thr-rich ), sequence variant (In CPCMR. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cleft palate, cardiac defects, and mental retardation (CPCMR) [MIM:600987]: An autosomal dominant disease characterized by multiple congenital malformations, mild-to-severe intellectual disability with poor speech, and delayed psychomotor development. Congenital malformations include heart defects, cleft lip/palate, distally-placed thumbs and toes, and cutaneous syndactyly between the second and third toes. {ECO:0000269|PubMed:24678003, ECO:0000269|PubMed:25712757, ECO:0000269|PubMed:27225850}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in transcriptional regulation. Binds to HOX or PBX proteins to form dimers, or to a DNA-bound dimer of PBX and HOX proteins and thought to have a role in stabilization of the homeoprotein-DNA complex. Isoform 3 is required for the activity of a PDX1:PBX1b:MEIS2b complex in pancreatic acinar cells involved in the transcriptional activation of the ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex (PTF1) bound to the enhancer A element; MEIS2 is not involved in complex DNA-binding. Probably in complex with PBX1, is involved in transcriptional regulation by KLF4. Isoform 3 and isoform 4 can bind to a EPHA8 promoter sequence containing the DNA motif 5'-CGGTCA-3'; in cooperation with a PBX protein (such as PBX2) is proposed to be involved in the transcriptional activation of EPHA8 in the developing midbrain. May be involved in regulation of myeloid differentiation. Can bind to the DNA sequence 5'-TGACAG-3'in the activator ACT sequence of the D(1A) dopamine receptor (DRD1) promoter and activate DRD1 transcription; isoform 5 cannot activate DRD1 transcription. {ECO:0000269|PubMed:10764806, ECO:0000269|PubMed:11279116, ECO:0000269|PubMed:21746878}.; ",{"$nulls":4},"p.Asp212Asn","c.634G>A","MODERATE","212/477",6,{"$nulls":5},"5","451","272","348","208","386","209","0","0","0","0.2297",{"$nulls":20},"3.515767","1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;.;.;1.54;.;1.54","1.355;1.355;.;.;.;.;.;1.355;1.355;.;.;.;.;.","1","-2.6;-2.6;-2.68;-2.53;-2.53;-2.47;-2.68;-2.58;-2.53;.;.;-3.65;.;-3.34","0.188;1.0;.;.;.;.;.;0.996;0.948;.;.;.;.;.","0.131;0.145;0.127;0.16;0.179;0.004;0.127;0.171;0.146;.;.;0.007;.;0.078","0.751;0.768;0.723;0.805;0.743;0.748;0.719;0.733;0.741;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1832950","0/0","450,0","0","450","0/1","203,64","0.2397","267",null,"chr15:37093586:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2356"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","MME","chr3:155180406","MME(H734Y)",null,null,"topological domain (Extracellular ), domain (Peptidase M13 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Charcot-Marie-Tooth disease 2T (CMT2T) [MIM:617017]: An axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. {ECO:0000269|PubMed:26991897, ECO:0000269|PubMed:27588448}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinocerebellar ataxia 43 (SCA43) [MIM:617018]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA43 is a slowly progressive, autosomal dominant form. {ECO:0000269|PubMed:27583304}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids (PubMed:15283675, PubMed:8168535). Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond (PubMed:17101991). Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9 (PubMed:15283675). Involved in the degradation of atrial natriuretic factor (ANF) (PubMed:2531377, PubMed:2972276). Displays UV-inducible elastase activity toward skin preelastic and elastic fibers (PubMed:20876573). {ECO:0000269|PubMed:15283675, ECO:0000269|PubMed:17101991, ECO:0000269|PubMed:20876573, ECO:0000269|PubMed:2531377, ECO:0000269|PubMed:27588448, ECO:0000269|PubMed:2972276}.; ",{"$nulls":4},"p.His734Tyr","c.2200C>T","MODERATE","734/750",23,{"$nulls":5},"5","295","228","194","161","265","199","0","0","0","0.3769",{"$nulls":20},"1.5829870000000001","-1.6;-1.6;-1.6;-1.6;-1.6;.","1.955","1","-2.74;-2.74;-2.74;-2.74;-2.74;.","0.031","0.08;0.08;0.08;0.08;0.08;.","0.196;0.176;0.176;0.224;0.298;0.185",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0270914| C4015635| C4310763","0/0","285,0","0","285","0/1","141,82","0.3677","223",null,"chr3:155180406:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3354"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","MTHFD1","chr14:64419883","MTHFD1(P285S)",null,null,"region of interest (Methylenetetrahydrofolate dehydrogenase and cyclohydrolase ), sequence variant (In CIMAH. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neural tube defects, folate-sensitive (NTDFS) [MIM:601634]: The most common NTDs are open spina bifida (myelomeningocele) and anencephaly. {ECO:0000269|PubMed:12384833, ECO:0000269|PubMed:16552426, ECO:0000269|PubMed:9611072}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:17000706}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; DISEASE: Combined immunodeficiency and megaloblastic anemia with or without hyperhomocysteinemia (CIMAH) [MIM:617780]: An autosomal recessive disorder due to an inborn error of folate metabolism. Variable clinical manifestations include hemolytic uremic syndrome, macrocytosis, epilepsy, hearing loss, retinopathy, mild mental retardation, and lymphopenia. {ECO:0000269|PubMed:21813566, ECO:0000269|PubMed:25633902, ECO:0000269|PubMed:27707659}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ",null,"mitocarta",{"$nulls":3},"p.Pro285Ser","c.853C>T","MODERATE","285/1020",8,{"$nulls":5},"5","590","375","403","260","555","347","0","0","0","0.1239",{"$nulls":20},"2.570894","0.35;.",null,"0.997999;0.997999;0.987927;0.987927","-5.15;.","0.08;.","0.06;.","0.34;0.346",{"$nulls":3},"Unknown",-1,"AR","Severe combined immunodeficiency","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Biochemical; Hematologic; Neurologic; Renal",null,"This gene encodes a protein that possesses three distinct enzymatic activities, 5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methenyltetrahydrofolate cyclohydrolase and 10-formyltetrahydrofolate synthetase. Each of these activities catalyzes one of three sequential reactions in the interconversion of 1-carbon derivatives of tetrahydrofolate, which are substrates for methionine, thymidylate, and de novo purine syntheses. The trifunctional enzymatic activities are conferred by two major domains, an aminoterminal portion containing the dehydrogenase and cyclohydrolase activities and a larger synthetase domain. [provided by RefSeq, Jul 2008].  ",null,"C1866558| C4540434","0/0","581,0","0","581","0/1","298,51","0.1461","349",null,"chr14:64419883:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1269"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","MTR","chr1:236852534","MTR(G570E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Homocystinuria-megaloblastic anemia, cblG complementation type (HMAG) [MIM:250940]: An autosomal recessive inborn error of metabolism resulting from defects in the cobalamin-dependent pathway that converts homocysteine to methionine. It causes delayed psychomotor development, megaloblastic anemia, homocystinuria, and hypomethioninemia. {ECO:0000269|PubMed:8968736, ECO:0000269|PubMed:8968737}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neural tube defects, folate-sensitive (NTDFS) [MIM:601634]: The most common NTDs are open spina bifida (myelomeningocele) and anencephaly. {ECO:0000269|PubMed:12375236}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the transfer of a methyl group from methyl- cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly570Glu","c.1709G>A","MODERATE","570/1265",17,{"$nulls":5},"5","988","1078","793","842","774","852","0","0","0","0.216",{"$nulls":20},"3.521069","-2.32","1.815;1.815;.","0.999947","-4.87;-4.87;-5.54",".;0.915;.","0.145;0.136;0.166","0.637;0.633;.",{"$nulls":3},"Unknown",-1,"AR","Methylmalonic acidemia, cblG type","Biochemical; Cardiovascular; Hematologic; Neurologic; Renal",{"$nulls":3},"C1855128| C1866558","0/0","973,0","0","973","0/1","838,194","0.188","1032",null,"chr1:236852534:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1793"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","MYO18B","chr22:25769220","MYO18B(G435E)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Klippel-Feil syndrome 4, autosomal recessive, with nemaline myopathy and facial dysmorphism (KFS4) [MIM:616549]: A form of Klippel-Feil syndrome, a skeletal disorder characterized by congenital fusion of cervical vertebrae. It is due to a failure in the normal segmentation of vertebrae during the early weeks of fetal development. The clinical triad consists of short neck, low posterior hairline, and limited neck movement. KFS4 features additionally include myopathy, mild short stature, microcephaly, and distinctive facies. {ECO:0000269|PubMed:25748484}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be involved in intracellular trafficking of the muscle cell when in the cytoplasm, whereas entering the nucleus, may be involved in the regulation of muscle specific genes. May play a role in the control of tumor development and progression; restored MYO18B expression in lung cancer cells suppresses anchorage-independent growth.; ",{"$nulls":4},"p.Gly435Glu","c.1304G>A","MODERATE","435/2568",4,{"$nulls":5},"5","458","368","359","287","393","313","0","0","0","0.1054",{"$nulls":20},"-0.002026","-1.9;-1.9;-1.92","-0.83","1","0.27","0.0;0.0;.","1.0","0.105;0.104;0.054",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225285","0/0","454,0","0","454","0/1","319,41","0.1139","360",null,"chr22:25769220:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1115"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","NANOS1","chr10:119030429","NANOS1(E210K)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spermatogenic failure 12 (SPGF12) [MIM:615413]: An infertility disorder caused by spermatogenesis defects. It results in decreased sperm motility, concentration, and multiple sperm structural defects. Non-obstructive azoospermia, oligozoospermia and oligo-astheno-teratozoospermia are features observed in SPGF12 patients. {ECO:0000269|PubMed:23315541}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May act as a translational repressor which regulates translation of specific mRNAs by forming a complex with PUM2 that associates with the 3'-UTR of mRNA targets. Capable of interfering with the proadhesive and anti-invasive functions of E-cadherin. Up-regulates the production of MMP14 to promote tumor cell invasion. {ECO:0000269|PubMed:17047063, ECO:0000269|PubMed:18223680}.; ",{"$nulls":4},"p.Glu210Lys","c.628G>A","MODERATE","210/292",1,{"$nulls":5},"5","303","276","224","205","182","144","0","0","0","0.3056",{"$nulls":20},"3.620079","0.88;0.82","1.83;.","0.995188","-0.73","0.958;.","0.091;0.173","0.131;.",{"$nulls":3},"Unknown",-1,"AD","Spermatogenic failure 12","Genitourinary",{"$nulls":3},"C3809427","0/0","270,0","0","270","0/1","190,55","0.2245","245",null,"chr10:119030429:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2293"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","NF1","chr17:31330457","NF1(L1924S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Neurofibromatosis 1 (NF1) [MIM:162200]: A disease characterized by patches of skin pigmentation (cafe-au-lait spots), Lisch nodules of the iris, tumors in the peripheral nervous system and fibromatous skin tumors. Individuals with the disorder have increased susceptibility to the development of benign and malignant tumors. {ECO:0000269|PubMed:10220149, ECO:0000269|PubMed:10336779, ECO:0000269|PubMed:10607834, ECO:0000269|PubMed:10712197, ECO:0000269|PubMed:10980545, ECO:0000269|PubMed:11258625, ECO:0000269|PubMed:11735023, ECO:0000269|PubMed:11857752, ECO:0000269|PubMed:12522551, ECO:0000269|PubMed:12552569, ECO:0000269|PubMed:12746402, ECO:0000269|PubMed:1302608, ECO:0000269|PubMed:15060124, ECO:0000269|PubMed:15146469, ECO:0000269|PubMed:15520408, ECO:0000269|PubMed:15523642, ECO:0000269|PubMed:15948193, ECO:0000269|PubMed:17160901, ECO:0000269|PubMed:21089070, ECO:0000269|PubMed:2114220, ECO:0000269|PubMed:21838856, ECO:0000269|PubMed:23758643, ECO:0000269|PubMed:24413922, ECO:0000269|PubMed:7981679, ECO:0000269|PubMed:8081387, ECO:0000269|PubMed:8544190, ECO:0000269|PubMed:8807336, ECO:0000269|PubMed:8834249, ECO:0000269|PubMed:9003501, ECO:0000269|PubMed:9101300, ECO:0000269|PubMed:9150739, ECO:0000269|PubMed:9298829, ECO:0000269|PubMed:9668168}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leukemia, juvenile myelomonocytic (JMML) [MIM:607785]: An aggressive pediatric myelodysplastic syndrome/myeloproliferative disorder characterized by malignant transformation in the hematopoietic stem cell compartment with proliferation of differentiated progeny. Patients have splenomegaly, enlarged lymph nodes, rashes, and hemorrhages. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Watson syndrome (WTSN) [MIM:193520]: A syndrome characterized by the presence of pulmonary stenosis, cafe-au-lait spots, and mental retardation. It is considered as an atypical form of neurofibromatosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Familial spinal neurofibromatosis (FSNF) [MIM:162210]: Considered to be an alternative form of neurofibromatosis, showing multiple spinal tumors. {ECO:0000269|PubMed:11704931}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neurofibromatosis-Noonan syndrome (NFNS) [MIM:601321]: Characterized by manifestations of both NF1 and Noonan syndrome (NS). NS is a disorder characterized by dysmorphic facial features, short stature, hypertelorism, cardiac anomalies, deafness, motor delay, and a bleeding diathesis. {ECO:0000269|PubMed:12707950, ECO:0000269|PubMed:16380919, ECO:0000269|PubMed:19845691}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. Note=The gene represented in this entry may be involved in disease pathogenesis.; ","FUNCTION: Stimulates the GTPase activity of Ras. NF1 shows greater affinity for Ras GAP, but lower specific activity. May be a regulator of Ras activity. {ECO:0000269|PubMed:2121371, ECO:0000269|PubMed:8417346}.; ","gedi|foundationOne|tcga-gbm|level2","[ \"Afatinib\" , \"Dabrafenib\" , \"Dasatinib\" , \"Erlotinib\" , \"Everolimus\" , \"Gefitinib\" , \"Lapatinib\" , \"Sirolimus\" , \"Temsirolimus\" , \"Trametinib\" , \"Tretinoin\" , \"Vandetanib\" , \"Vemurafenib\"]","[ \"Afatinib\" , \"Dabrafenib\" , \"Dasatinib\" , \"Erlotinib\" , \"Everolimus\" , \"Gefitinib\" , \"Lapatinib\" , \"Sirolimus\" , \"Temsirolimus\" , \"Trametinib\" , \"Tretinoin\" , \"Vandetanib\" , \"Vemurafenib\"]","[ \"Afatinib\" , \"Dabrafenib\" , \"Dasatinib\" , \"Erlotinib\" , \"Everolimus\" , \"Gefitinib\" , \"Lapatinib\" , \"Sirolimus\" , \"Temsirolimus\" , \"Trametinib\" , \"Tretinoin\" , \"Vandetanib\" , \"Vemurafenib\"]","p.Leu1924Ser","c.5771T>C","MODERATE","1924/2839",39,{"$nulls":5},"5","492","390","338","255","467","365","0","0","0","0.2658",{"$nulls":20},"4.093202","-4.43;-4.43;-4.43;.","1.905;.;.;.","0.999999","-5.18;-5.18;-4.98;.","0.885;0.997;.;.","0.0;0.0;0.0;.","0.953;0.952;.;.",{"$nulls":3},"Unknown",-1,"AD","Neurofibromatosis type 1, Neurofibromatosis-Noonan syndrome; Watson syndrome","Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic","COSMIC,kMAPK,vRTK","This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008].",null,"C0553586| C0349639| C0027831| C2931482| C1834235","0/0","484,0","0","484","0/1","275,100","0.2667","375",null,"chr17:31330457:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2902"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","NPC1","chr18:23561395","NPC1(G199E)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Niemann-Pick disease C1 (NPC1) [MIM:257220]: A lysosomal storage disorder that affects the viscera and the central nervous system. It is due to defective intracellular processing and transport of low-density lipoprotein derived cholesterol. It causes accumulation of cholesterol in lysosomes, with delayed induction of cholesterol homeostatic reactions. Niemann-Pick disease type C1 has a highly variable clinical phenotype. Clinical features include variable hepatosplenomegaly and severe progressive neurological dysfunction such as ataxia, dystonia and dementia. The age of onset can vary from infancy to late adulthood. An allelic variant of Niemann-Pick disease type C1 is found in people with Nova Scotia ancestry. Patients with the Nova Scotian clinical variant are less severely affected. {ECO:0000269|PubMed:10480349, ECO:0000269|PubMed:10521290, ECO:0000269|PubMed:10521297, ECO:0000269|PubMed:11182931, ECO:0000269|PubMed:11333381, ECO:0000269|PubMed:11349231, ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11545687, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:12408188, ECO:0000269|PubMed:12554680, ECO:0000269|PubMed:12955717, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014, ECO:0000269|PubMed:16126423, ECO:0000269|PubMed:16802107, ECO:0000269|PubMed:27238017, ECO:0000269|PubMed:9211849, ECO:0000269|PubMed:9634529}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Intracellular cholesterol transporter which acts in concert with NPC2 and plays an important role in the egress of cholesterol from the endosomal/lysosomal compartment (PubMed:9211849, PubMed:9927649, PubMed:10821832, PubMed:18772377, PubMed:27238017, PubMed:12554680). Unesterified cholesterol that has been released from LDLs in the lumen of the late endosomes/lysosomes is transferred by NPC2 to the cholesterol- binding pocket in the N-terminal domain of NPC1 (PubMed:9211849, PubMed:9927649, PubMed:18772377, PubMed:19563754, PubMed:27238017, PubMed:28784760). Cholesterol binds to NPC1 with the hydroxyl group buried in the binding pocket (PubMed:19563754). Binds oxysterol with higher affinity than cholesterol. May play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural and functional integrity of nerve terminals (Probable). {ECO:0000269|PubMed:10821832, ECO:0000269|PubMed:12554680, ECO:0000269|PubMed:18772377, ECO:0000269|PubMed:19563754, ECO:0000269|PubMed:27238017, ECO:0000269|PubMed:28784760, ECO:0000269|PubMed:9211849, ECO:0000269|PubMed:9927649, ECO:0000305}.; ",{"$nulls":5},"c.596G>A","HIGH",null,5,{"$nulls":5},"5","605","486","461","373","511","419","0","0","0","0.2243",{"$nulls":20},"2.275167","-2.64","2.41","1","-4.13","0.006","0.212","0.561",{"$nulls":3},"Unknown",-1,"AR","Niemann-Pick disease, type C1; Niemann-Pick disease, type D ","Biochemical; Gastrointestinal; Neurologic; Ophthalmologic",{"$nulls":3},"C3179455","0/0","596,0","0","596","0/1","370,99","0.2111","469",null,"chr18:23561395:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2011"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","NUP133","chr1:229498252","NUP133(E235K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in poly(A)+ RNA transport. {ECO:0000269|PubMed:11684705}.; ",{"$nulls":4},"p.Glu235Lys","c.703G>A","MODERATE","235/1156",6,{"$nulls":5},"5","302","308","189","201","278","277","0","0","0","0.0794",{"$nulls":20},"2.374531","1.02","2.34","0.999482;0.998792;0.999886","-1.13","0.081","0.132","0.229",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748549| C5193045","0/0","299,0","0","299","0/1","274,26","0.0867","300",null,"chr1:229498252:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0995"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","OOSP2","chr11:60043547","OOSP2(A48V)",{"$nulls":6},255,"PASS","Missense","rs375351184",1.1641443538998837E-4,{"$nulls":6},"p.Ala48Val","c.143C>T","MODERATE","48/158",2,2,{"$nulls":4},"5","429","342","300","242","384","302","0","0","0","0.1126",{"$nulls":20},"1.489266","-1.56","1.735;.","1","-1.04","0.995;.","0.162;0.296","0.488;0.436",{"$nulls":3},"ESP6500_EA_AF",1.1641443538998837E-4,{"$nulls":7},"0/0","408,0","0","408","0/1","288,38","0.1166","326",null,"chr11:60043547:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1198"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","OR10A5","chr11:6846031","OR10A5(A117T)",null,null,"transmembrane region (Helical; Name=3 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor (Potential). May be involved in taste perception. {ECO:0000305}.; ",{"$nulls":4},"p.Ala117Thr","c.349G>A","MODERATE","117/317",1,{"$nulls":5},"5","827","603","693","497","714","519","0","0","0","0.2254",{"$nulls":20},"1.847043","4.5","1.535","0.536165","-1.28","0.079","0.234","0.102",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","824,0","0","824","0/1","464,133","0.2228","597",null,"chr11:6846031:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2233"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","OR5A2","chr11:59422181","OR5A2(F258Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Phe258Tyr","c.773T>A","MODERATE","258/324",1,{"$nulls":5},"4","434","362","335","284","370","317","0.0023","0.0023","0","0.2555",{"$nulls":20},"3.27737","8.33;.;.","1.025","0.999693","-2.29;.;.","1.0","0.055;.;.","0.368;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","431,1","0.0023","432","0/1","270,89","0.2479","359",null,"chr11:59422181:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2359"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PAM","chr5:103025280","PAM(V879I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Bifunctional enzyme that catalyzes 2 sequential steps in C-terminal alpha-amidation of peptides. The monooxygenase part produces an unstable peptidyl(2-hydroxyglycine) intermediate that is dismutated to glyoxylate and the corresponding desglycine peptide amide by the lyase part. C-terminal amidation of peptides such as neuropeptides is essential for full biological activity.; ",{"$nulls":4},"p.Val879Ile","c.2635G>A","MODERATE","879/974",23,{"$nulls":5},"5","256","186","175","128","236","165","0","0","0","0.1758",{"$nulls":20},"2.583857","0.89;0.74;0.88","2.125;.;2.125","0.993661;0.993654;0.988736;0.993654;0.995091;1;1","-0.21;-0.01;-0.24","0.93;0.928;0.545","0.129;0.221;0.285","0.224;0.206;0.231",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","251,0","0","251","0/1","150,33","0.1803","183",null,"chr5:103025280:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1797"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PEG3","chr19:56813968","PEG3(E1492Q)",null,null,"compositionally biased region (Glu-rich ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs747031416",6.056e-05,null,"FUNCTION: Induces apoptosis in cooperation with SIAH1A. Acts as a mediator between p53/TP53 and BAX in a neuronal death pathway that is activated by DNA damage. Acts synergistically with TRAF2 and inhibits TNF induced apoptosis through activation of NF-kappa-B (By similarity). Possesses a tumor suppressing activity in glioma cells. {ECO:0000250, ECO:0000269|PubMed:11260267}.; ",{"$nulls":4},"p.Glu1492Gln","c.4474G>C","MODERATE","1492/1588",10,{"$nulls":5},"4","578","508","440","390","436","379","0","0","0","0.1741",{"$nulls":20},"3.080358","3.98;.;.;.;.;.;.;.;.;3.82;3.84;3.98;3.98","2.19;.;.;.;.;.;.;.;.;.;.;2.19;2.19",null,"-1.1;.;.;.;.;.;.;.;.;.;.;.;.","0.995;.;.;.;.;.;.;.;.;.;.;0.995;0.995","0.021;.;.;.;.;.;.;.;.;.;.;.;.","0.078;.;.;.;.;.;.;.;.;0.132;0.121;.;.",{"$nulls":3},"ExAC_SAS_AF",6.056e-05,{"$nulls":7},"0/0","574,0","0","574","0/1","408,84","0.1707","492",null,"chr19:56813968:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1769"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PKD1","chr16:2111183","PKD1(W1328*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Polycystic kidney disease 1 with or without polycystic liver disease (PKD1) [MIM:173900]: An autosomal dominant disorder characterized by renal cysts, liver cysts and intracranial aneurysm. Clinical variability is due to differences in the rate of loss of glomerular filtration, the age of reaching end-stage renal disease and the occurrence of hypertension, symptomatic extrarenal cysts, and subarachnoid hemorrhage from intracranial 'berry' aneurysm. {ECO:0000269|PubMed:10200984, ECO:0000269|PubMed:10364515, ECO:0000269|PubMed:10577909, ECO:0000269|PubMed:10647901, ECO:0000269|PubMed:10729710, ECO:0000269|PubMed:10854095, ECO:0000269|PubMed:10923040, ECO:0000269|PubMed:10987650, ECO:0000269|PubMed:11012875, ECO:0000269|PubMed:11058904, ECO:0000269|PubMed:11115377, ECO:0000269|PubMed:11216660, ECO:0000269|PubMed:11316854, ECO:0000269|PubMed:11558899, ECO:0000269|PubMed:11571556, ECO:0000269|PubMed:11691639, ECO:0000269|PubMed:11773467, ECO:0000269|PubMed:11857740, ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:12007219, ECO:0000269|PubMed:12070253, ECO:0000269|PubMed:12220456, ECO:0000269|PubMed:12482949, ECO:0000269|PubMed:12842373, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007, ECO:0000269|PubMed:21115670, ECO:0000269|PubMed:22508176, ECO:0000269|PubMed:8554072, ECO:0000269|PubMed:9199561, ECO:0000269|PubMed:9259200, ECO:0000269|PubMed:9285784, ECO:0000269|PubMed:9521593, ECO:0000269|PubMed:9921908}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in renal tubulogenesis (PubMed:12482949). Involved in fluid-flow mechanosensation by the primary cilium in renal epithelium (By similarity). Acts as a regulator of cilium length, together with PKD2 (By similarity). The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling (By similarity). The cilium length response creates a negative feedback loop whereby fluid shear- mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling (By similarity). May be an ion-channel regulator. Involved in adhesive protein-protein and protein- carbohydrate interactions. {ECO:0000250|UniProtKB:O08852, ECO:0000269|PubMed:12482949}.; ",{"$nulls":4},"p.Trp1328*","c.3984G>A","HIGH","1328/4303",15,{"$nulls":5},"4","1784","1422","1275","1000","1664","1290","0","0","0","0.1248",{"$nulls":5},"(PKD1|ENSG00000008710|1|1.00)","(PKD1|ENSG00000008710|1|1.00)",{"$nulls":13},"8.652765",null,null,"1",{"$nulls":3},"0.769;0.764",{"$nulls":3},"Unknown",-1,"AD","Polycystic kidney disease, adult type I","Cardiovascular; Gastrointestinal; Renal",{"$nulls":3},"C3149841","0/0","1670,0","0","1670","0/1","1153,173","0.1305","1326",null,"chr16:2111183:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.125"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PKLR","chr1:155294306","PKLR(V349I)",null,null,"helix ","helix:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Pyruvate kinase hyperactivity (PKHYP) [MIM:102900]: Autosomal dominant phenotype characterized by increase of red blood cell ATP. {ECO:0000269|PubMed:9090535}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pyruvate kinase deficiency of red cells (PKRD) [MIM:266200]: A frequent cause of hereditary non-spherocytic hemolytic anemia. Clinically, pyruvate kinase-deficient patients suffer from a highly variable degree of chronic hemolysis, ranging from severe neonatal jaundice and fatal anemia at birth, severe transfusion-dependent chronic hemolysis, moderate hemolysis with exacerbation during infection, to a fully compensated hemolysis without apparent anemia. {ECO:0000269|PubMed:11328279, ECO:0000269|PubMed:11960989, ECO:0000269|PubMed:1536957, ECO:0000269|PubMed:1896471, ECO:0000269|PubMed:19085939, ECO:0000269|PubMed:2018831, ECO:0000269|PubMed:21794208, ECO:0000269|PubMed:7706479, ECO:0000269|PubMed:8161798, ECO:0000269|PubMed:8180378, ECO:0000269|PubMed:8476433, ECO:0000269|PubMed:8481523, ECO:0000269|PubMed:8483951, ECO:0000269|PubMed:9482576, ECO:0000269|PubMed:9827908, ECO:0000269|PubMed:9886305, ECO:0000269|Ref.24}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a key role in glycolysis. {ECO:0000250}.; ",{"$nulls":4},"p.Val349Ile","c.1045G>A","MODERATE","349/574",7,{"$nulls":5},"5","542","642","410","495","473","560","0","0","0","0.2304",{"$nulls":20},"3.744189","-6.08","2.205;.","1","-0.95;-0.94","0.873;.","0.001","0.669;0.663",{"$nulls":3},"Unknown",-1,"AR","Pyruvate kinase deficiency","Hematologic",{"$nulls":3},"C0340968| C1863224","0/0","525,0","0","525","0/1","456,148","0.245","604",null,"chr1:155294306:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2404"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PLOD1","chr1:11970773","PLOD1(I620S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Ehlers-Danlos syndrome, kyphoscoliotic type, 1 (EDSKSCL1) [MIM:225400]: A form of Ehlers-Danlos syndrome, a group of connective tissue disorders characterized by skin hyperextensibility, articular hypermobility, and tissue fragility. EDSKSCL1 is an autosomal recessive form characterized by severe muscle hypotonia at birth, generalized joint laxity, scoliosis at birth, and scleral fragility and rupture of the ocular globe. {ECO:0000269|PubMed:10686424, ECO:0000269|PubMed:15666309, ECO:0000269|PubMed:15854030, ECO:0000269|PubMed:15979919, ECO:0000269|PubMed:8163671, ECO:0000269|PubMed:9617436}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils (By similarity). Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens (PubMed:8621606, PubMed:10686424, PubMed:15854030). These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links (Probable). {ECO:0000250|UniProtKB:Q9R0E2, ECO:0000269|PubMed:10686424, ECO:0000269|PubMed:15854030, ECO:0000269|PubMed:8621606, ECO:0000305}.; ",{"$nulls":4},"p.Ile620Ser","c.1859T>G","MODERATE","620/727",17,{"$nulls":5},"5","741","591","479","387","690","542","0","0","0","0.107",{"$nulls":20},"3.630988","-0.35","2.215","1","-4.97","0.434","0.001","0.931",{"$nulls":3},"Unknown",-1,"AR","Ehlers-Danlos syndrome type VI","Cardiovascular; Dermatologic; Musculoskeletal; Ophthalmologic; Renal",{"$nulls":3},"C0268342","0/0","718,0","0","718","0/1","490,60","0.1091","550",null,"chr1:11970773:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1111"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PSD4","chr2:113182697","PSD4(Q81*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Guanine nucleotide exchange factor for ARF6 and ARL14/ARF7. Through ARL14 activation, controls the movement of MHC class II-containing vesicles along the actin cytoskeleton in dendritic cells. Involved in membrane recycling. Interacts with several phosphatidylinositol phosphate species, including phosphatidylinositol 3,4-bisphosphate, phosphatidylinositol 3,5- bisphosphate and phosphatidylinositol 4,5-bisphosphate. {ECO:0000269|PubMed:12082148, ECO:0000269|PubMed:21458045}.; ",{"$nulls":4},"p.Gln81*","c.241C>T","HIGH","81/1056",2,{"$nulls":5},"5","407","317","322","261","146","124","0","0","0","0.25",{"$nulls":5},"(PSD4|ENSG00000125637|1|1.00)","(PSD4|ENSG00000125637|1|1.00)",{"$nulls":13},"4.068926",null,null,"1",{"$nulls":3},"0.051;0.052",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","406,0","0","406","0/1","240,69","0.2233","309",null,"chr2:113182697:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2375"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PTEN","chr10:87894051","PTEN(G36R)",null,null,"domain (Phosphatase tensin-type ), sequence variant (In glioma; dbSNP:rs1554893792. PTEN(G36E)), sequence variant (In endometrial hyperplasia; dbSNP:rs786204854. PTEN(G36R))",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cowden syndrome 1 (CWS1) [MIM:158350]: An autosomal dominant hamartomatous polyposis syndrome with age-related penetrance. Cowden syndrome is characterized by hamartomatous lesions affecting derivatives of ectodermal, mesodermal and endodermal layers, macrocephaly, facial trichilemmomas (benign tumors of the hair follicle infundibulum), acral keratoses, papillomatous papules, and elevated risk for development of several types of malignancy, particularly breast carcinoma in women and thyroid carcinoma in both men and women. Colon cancer and renal cell carcinoma have also been reported. Hamartomas can be found in virtually every organ, but most commonly in the skin, gastrointestinal tract, breast and thyroid. {ECO:0000269|PubMed:10051160, ECO:0000269|PubMed:10234502, ECO:0000269|PubMed:10400993, ECO:0000269|PubMed:10866302, ECO:0000269|PubMed:11230179, ECO:0000269|PubMed:11494117, ECO:0000269|PubMed:15355975, ECO:0000269|PubMed:18716620, ECO:0000269|PubMed:9140396, ECO:0000269|PubMed:9241266, ECO:0000269|PubMed:9259288, ECO:0000269|PubMed:9345101, ECO:0000269|PubMed:9399897, ECO:0000269|PubMed:9425889, ECO:0000269|PubMed:9467011, ECO:0000269|PubMed:9600246, ECO:0000269|PubMed:9735393, ECO:0000269|PubMed:9797362, ECO:0000269|PubMed:9811831, ECO:0000269|PubMed:9832031, ECO:0000269|PubMed:9915974}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Lhermitte-Duclos disease (LDD) [MIM:158350]: A rare disease characterized by the occurrence of a slowly enlarging mass within the cerebellar cortex corresponding histologically to a cerebellar hamartoma. It manifests, most commonly in the third and fourth decades of life, with increased intracranial pressure, headache, nausea, cerebellar dysfunction, occlusive hydrocephalus, ataxia, visual disturbances and other cranial nerve palsies. Various associated abnormalities may be present such as megalencephaly, microgyria, hydromyelia, polydactyly, partial gigantism, macroglossia. LDD is part of the PTEN hamartoma tumor syndromes spectrum that also includes Cowden syndrome. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. {ECO:0000269|PubMed:11801303}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Endometrial cancer (ENDMC) [MIM:608089]: A malignancy of endometrium, the mucous lining of the uterus. Most endometrial cancers are adenocarcinomas, cancers that begin in cells that make and release mucus and other fluids. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Note=PTEN mutations are found in a subset of patients with Proteus syndrome, a genetically heterogeneous condition. The molecular diagnosis of PTEN mutation positive cases classifies Proteus syndrome patients as part of the PTEN hamartoma syndrome spectrum. As such, patients surviving the early years of Proteus syndrome are likely at a greater risk of developing malignancies.; DISEASE: Glioma 2 (GLM2) [MIM:613028]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269|PubMed:12085208}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Prostate cancer (PC) [MIM:176807]: A malignancy originating in tissues of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269|PubMed:26504226, ECO:0000269|PubMed:9072974}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Macrocephaly/autism syndrome (MCEPHAS) [MIM:605309]: Patients have autism spectrum disorders and macrocephaly, with head circumferences ranging from +2.5 to +8 SD for age and sex (average head circumference +4.0 SD). {ECO:0000269|PubMed:15805158, ECO:0000269|PubMed:23160955, ECO:0000269|PubMed:26637798}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A microdeletion of chromosome 10q23 involving BMPR1A and PTEN is a cause of chromosome 10q23 deletion syndrome, which shows overlapping features of the following three disorders: Bannayan-Zonana syndrome, Cowden disease and juvenile polyposis syndrome.; ","FUNCTION: Tumor suppressor. Acts as a dual-specificity protein phosphatase, dephosphorylating tyrosine-, serine- and threonine- phosphorylated proteins. Also acts as a lipid phosphatase, removing the phosphate in the D3 position of the inositol ring from phosphatidylinositol 3,4,5-trisphosphate, phosphatidylinositol 3,4-diphosphate, phosphatidylinositol 3- phosphate and inositol 1,3,4,5-tetrakisphosphate with order of substrate preference in vitro PtdIns(3,4,5)P3 > PtdIns(3,4)P2 > PtdIns3P > Ins(1,3,4,5)P4 (PubMed:26504226). The lipid phosphatase activity is critical for its tumor suppressor function. Antagonizes the PI3K-AKT/PKB signaling pathway by dephosphorylating phosphoinositides and thereby modulating cell cycle progression and cell survival. The unphosphorylated form cooperates with AIP1 to suppress AKT1 activation. Dephosphorylates tyrosine-phosphorylated focal adhesion kinase and inhibits cell migration and integrin-mediated cell spreading and focal adhesion formation. Plays a role as a key modulator of the AKT-mTOR signaling pathway controlling the tempo of the process of newborn neurons integration during adult neurogenesis, including correct neuron positioning, dendritic development and synapse formation. May be a negative regulator of insulin signaling and glucose metabolism in adipose tissue. The nuclear monoubiquitinated form possesses greater apoptotic potential, whereas the cytoplasmic nonubiquitinated form induces less tumor suppressive ability. In motile cells, suppresses the formation of lateral pseudopods and thereby promotes cell polarization and directed movement. {ECO:0000269|PubMed:26504226}.; ","gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Afatinib\" , \"Bevacizumab\" , \"Cetuximab\" , \"Chlorpromazine\" , \"Dabrafenib\" , \"Erlotinib\" , \"Everolimus\" , \"Gefitinib\" , \"Lapatinib\" , \"Metformin\" , \"Nelfinavir\" , \"Olaparib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Sirolimus\" , \"Sorafenib\" , \"Sunitinib\" , \"Temozolomide\" , \"Temsirolimus\" , \"Trastuzumab\" , \"Vemurafenib\"]","[ \"Afatinib\" , \"Bevacizumab\" , \"Cetuximab\" , \"Chlorpromazine\" , \"Dabrafenib\" , \"Erlotinib\" , \"Everolimus\" , \"Gefitinib\" , \"Lapatinib\" , \"Metformin\" , \"Nelfinavir\" , \"Olaparib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Sirolimus\" , \"Sorafenib\" , \"Sunitinib\" , \"Temozolomide\" , \"Temsirolimus\" , \"Trastuzumab\" , \"Vemurafenib\"]","[ \"Afatinib\" , \"Bevacizumab\" , \"Cetuximab\" , \"Chlorpromazine\" , \"Dabrafenib\" , \"Erlotinib\" , \"Everolimus\" , \"Gefitinib\" , \"Lapatinib\" , \"Metformin\" , \"Nelfinavir\" , \"Olaparib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Sirolimus\" , \"Sorafenib\" , \"Sunitinib\" , \"Temozolomide\" , \"Temsirolimus\" , \"Trastuzumab\" , \"Vemurafenib\"]","p.Gly36Arg","c.106G>A","MODERATE","36/403",2,11,{"$nulls":4},"5","582","392","419","290","501","332","0","0","0","0.2229",{"$nulls":20},"4.235872","-5.11","3.64","1","-7.78","1.0",null,"0.987",{"$nulls":3},"Unknown",-1,"AD","PTEN hamartoma tumor syndrome; Cowden syndrome; Bannayan-Riley-Ruvalcaba syndrome; Lhermitte-Duclos syndrome; Glioma susceptibility 2; Meningioma, familial; Endometrial cancer","Craniofacial; Dermatologic; Neurologic; Oncologic","COSMIC,kCANCER,kP53,vpi3k,vpi3k",null,null,"C1854416| C0376358| CN072330| C2751642| C1959582| C3551915","0/0","569,0","0","569","0/1","302,78","0.2053","380",null,"chr10:87894051:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2034"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","PTPRG","chr3:62168038","PTPRG(R303K)",null,null,"topological domain (Extracellular ), domain (Alpha-carbonic anhydrase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Possesses tyrosine phosphatase activity. {ECO:0000269|PubMed:19167335}.; ",{"$nulls":4},"p.Arg303Lys","c.908G>A","MODERATE","303/1445",8,{"$nulls":5},"4","440","337","327","251","374","283","0","0","0","0.2155",{"$nulls":20},"3.958551","-0.13","1.235","0.999998","-0.97","0.756;0.795","0.008;0.007","0.588;0.728",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","435,0","0","435","0/1","259,74","0.2222","333",null,"chr3:62168038:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2112"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RASAL3","chr19:15457345","RASAL3(E460K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a Ras GTPase-activating protein. Plays an important role in the expansion and functions of natural killer T (NKT) cells in the liver by negatively regulating RAS activity and the down-stream ERK signaling pathway. {ECO:0000250|UniProtKB:Q8C2K5}.; ",{"$nulls":4},"p.Glu460Lys","c.1378G>A","MODERATE","460/1011",9,{"$nulls":5},"5","304","274","253","224","226","204","0","0","0","0.098",{"$nulls":20},"3.186177","-1.69","2.625","0.999999","-3.53","0.539","0.001","0.55",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","299,0","0","299","0/1","243,26","0.0967","269",null,"chr19:15457345:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0893"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RASGRP4","chr19:38414876","RASGRP4(A401V)",{"$nulls":6},255,"PASS","Missense","rs569953333",1.440922190201729E-3,null,"FUNCTION: Functions as a cation- and diacylglycerol (DAG)- regulated nucleotide exchange factor activating Ras through the exchange of bound GDP for GTP. May function in mast cells differentiation. {ECO:0000269|PubMed:11880369, ECO:0000269|PubMed:11956218, ECO:0000269|PubMed:12493770, ECO:0000269|PubMed:18024961}.; ","level2",{"$nulls":3},"p.Ala401Val","c.1202C>T","MODERATE","401/673",9,{"$nulls":5},"4","531","420","459","358","426","342","0","0","0","0.1287",{"$nulls":20},"2.59577","1.57;1.57;1.57;.;.;1.57;.;1.57",".;.;.;.;.;.;1.89;1.89","0.999815;0.83045;0.999815;0.999815;0.999815;1;1",".;.;.;.;.;-2.89;.;.","0.301;.;.;.;.;.;0.022;0.022",".;.;.;.;.;0.09;.;.","0.273;0.432;0.289;0.253;0.252;0.253;0.245;0.243",{"$nulls":3},"1000Gp3_AMR_AF",1.440922190201729E-3,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","530,0","0","530","0/1","358,53","0.129","411",null,"chr19:38414876:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1257"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RB1","chr13:48360028","RB1(Q207*)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,"DISEASE: Childhood cancer retinoblastoma (RB) [MIM:180200]: Congenital malignant tumor that arises from the nuclear layers of the retina. It occurs in about 1:20'000 live births and represents about 2% of childhood malignancies. It is bilateral in about 30% of cases. Although most RB appear sporadically, about 20% are transmitted as an autosomal dominant trait with incomplete penetrance. The diagnosis is usually made before the age of 2 years when strabismus or a gray to yellow reflex from pupil ('cat eye') is investigated. {ECO:0000269|PubMed:10671068, ECO:0000269|PubMed:11524739, ECO:0000269|PubMed:1352883, ECO:0000269|PubMed:2594029, ECO:0000269|PubMed:7704558, ECO:0000269|PubMed:7795591, ECO:0000269|PubMed:7927327, ECO:0000269|PubMed:8346255, ECO:0000269|PubMed:8605116, ECO:0000269|PubMed:8776589, ECO:0000269|PubMed:9140452, ECO:0000269|PubMed:9311732, ECO:0000269|PubMed:9973307}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Osteogenic sarcoma (OSRC) [MIM:259500]: A sarcoma originating in bone-forming cells, affecting the ends of long bones. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key regulator of entry into cell division that acts as a tumor suppressor. Promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. Acts as a transcription repressor of E2F1 target genes. The underphosphorylated, active form of RB1 interacts with E2F1 and represses its transcription activity, leading to cell cycle arrest. Directly involved in heterochromatin formation by maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin by stabilizing histone methylation. Recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. Controls histone H4 'Lys-20' trimethylation. Inhibits the intrinsic kinase activity of TAF1. Mediates transcriptional repression by SMARCA4/BRG1 by recruiting a histone deacetylase (HDAC) complex to the c-FOS promoter. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex (By similarity). In case of viral infections, interactions with SV40 large T antigen, HPV E7 protein or adenovirus E1A protein induce the disassembly of RB1-E2F1 complex thereby disrupting RB1's activity. {ECO:0000250, ECO:0000269|PubMed:15084261}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Palbociclib\" , \"Palbociclib\"]","[ \"Palbociclib\" , \"Palbociclib\"]","[ \"Palbociclib\" , \"Palbociclib\"]","p.Gln207*","c.619C>T","HIGH","207/928",7,{"$nulls":5},"5","511","311","392","249","392","216","0","0","0","0.162",{"$nulls":5},"(RB1|ENSG00000139687|1|1.00)","(RB1|ENSG00000139687|1|1.00)",{"$nulls":13},"7.326259",null,null,"1",{"$nulls":3},"0.965;.",{"$nulls":3},"Unknown",-1,"AD","Retinoblastoma","Oncologic","COSMIC,kCANCER,kCELL_CYCLE,vRB",null,null,"C0029463| C0035335| C0005684| C0149925| C0149925","0/0","495,0","0","495","0/1","251,54","0.177","305",null,"chr13:48360028:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1807"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RB1","chr13:48456239","RB1(G617D)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Childhood cancer retinoblastoma (RB) [MIM:180200]: Congenital malignant tumor that arises from the nuclear layers of the retina. It occurs in about 1:20'000 live births and represents about 2% of childhood malignancies. It is bilateral in about 30% of cases. Although most RB appear sporadically, about 20% are transmitted as an autosomal dominant trait with incomplete penetrance. The diagnosis is usually made before the age of 2 years when strabismus or a gray to yellow reflex from pupil ('cat eye') is investigated. {ECO:0000269|PubMed:10671068, ECO:0000269|PubMed:11524739, ECO:0000269|PubMed:1352883, ECO:0000269|PubMed:2594029, ECO:0000269|PubMed:7704558, ECO:0000269|PubMed:7795591, ECO:0000269|PubMed:7927327, ECO:0000269|PubMed:8346255, ECO:0000269|PubMed:8605116, ECO:0000269|PubMed:8776589, ECO:0000269|PubMed:9140452, ECO:0000269|PubMed:9311732, ECO:0000269|PubMed:9973307}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Osteogenic sarcoma (OSRC) [MIM:259500]: A sarcoma originating in bone-forming cells, affecting the ends of long bones. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key regulator of entry into cell division that acts as a tumor suppressor. Promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. Acts as a transcription repressor of E2F1 target genes. The underphosphorylated, active form of RB1 interacts with E2F1 and represses its transcription activity, leading to cell cycle arrest. Directly involved in heterochromatin formation by maintaining overall chromatin structure and, in particular, that of constitutive heterochromatin by stabilizing histone methylation. Recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. Controls histone H4 'Lys-20' trimethylation. Inhibits the intrinsic kinase activity of TAF1. Mediates transcriptional repression by SMARCA4/BRG1 by recruiting a histone deacetylase (HDAC) complex to the c-FOS promoter. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex (By similarity). In case of viral infections, interactions with SV40 large T antigen, HPV E7 protein or adenovirus E1A protein induce the disassembly of RB1-E2F1 complex thereby disrupting RB1's activity. {ECO:0000250, ECO:0000269|PubMed:15084261}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Palbociclib\" , \"Palbociclib\"]","[ \"Palbociclib\" , \"Palbociclib\"]","[ \"Palbociclib\" , \"Palbociclib\"]","p.Gly617Asp","c.1850G>A","MODERATE","617/928",19,{"$nulls":5},"4","268","203","199","154","203","139","0","0","0","0.0791",{"$nulls":20},"1.756951","-2.93;.","0.895;.","0.97907","-0.59;.","0.062;.","0.595;.","0.325;.",{"$nulls":3},"Unknown",-1,"AD","Retinoblastoma","Oncologic","COSMIC,kCANCER,kCELL_CYCLE,vRB",null,null,"C0029463| C0035335| C0005684| C0149925| C0149925","0/0","261,0","0","261","0/1","174,18","0.0938","192",null,"chr13:48456239:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0909"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RELN","chr7:103698023","RELN(Q325*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lissencephaly 2 (LIS2) [MIM:257320]: A classic type lissencephaly associated with ataxia, mental retardation, seizures and abnormalities of the cerebellum, hippocampus and brainstem. {ECO:0000269|PubMed:10973257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epilepsy, familial temporal lobe, 7 (ETL7) [MIM:616436]: A focal form of epilepsy characterized by recurrent seizures that arise from foci within the temporal lobe. Seizures are usually accompanied by sensory symptoms, most often auditory in nature. {ECO:0000269|PubMed:26046367}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Extracellular matrix serine protease that plays a role in layering of neurons in the cerebral cortex and cerebellum. Regulates microtubule function in neurons and neuronal migration. Affects migration of sympathetic preganglionic neurons in the spinal cord, where it seems to act as a barrier to neuronal migration. Enzymatic activity is important for the modulation of cell adhesion. Binding to the extracellular domains of lipoprotein receptors VLDLR and LRP8/APOER2 induces tyrosine phosphorylation of DAB1 and modulation of TAU phosphorylation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gln325*","c.973C>T","HIGH","325/3460",10,2,{"$nulls":4},"5","670","477","506","345","593","415","0","0","0","0.2193",{"$nulls":5},"(RELN|ENSG00000189056|1|1.00)","(RELN|ENSG00000189056|1|1.00)",{"$nulls":13},"7.680935",null,null,"1",{"$nulls":3},"0.782;0.782;0.783",{"$nulls":3},"Unknown",-1,"AR","Lissencephaly 2","Craniofacial; Neurologic",{"$nulls":3},"C4551957| C0796089| C4225327","0/0","651,0","0","651","0/1","358,104","0.2251","462",null,"chr7:103698023:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2058"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RSPO2","chr8:108082626","RSPO2(L5F)",null,null,"signal peptide , splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs555188515",4.513e-05,null,"FUNCTION: Activator of the canonical Wnt signaling pathway by acting as a ligand for LGR4-6 receptors. Upon binding to LGR4-6 (LGR4, LGR5 or LGR6), LGR4-6 associate with phosphorylated LRP6 and frizzled receptors that are activated by extracellular Wnt receptors, triggering the canonical Wnt signaling pathway to increase expression of target genes. Also regulates the canonical Wnt/beta-catenin-dependent pathway and non-canonical Wnt signaling by acting as an inhibitor of ZNRF3, an important regulator of the Wnt signaling pathway. Probably also acts as a ligand for frizzled and LRP receptors. {ECO:0000269|PubMed:21727895, ECO:0000269|PubMed:21909076, ECO:0000269|PubMed:22615920}.; ","gedi",{"$nulls":3},"p.Leu5Phe","c.13C>T","MODERATE","5/243",2,{"$nulls":5},"5","446","344","295","237","407","306","0","0","0","0.098",{"$nulls":20},"4.290394","-1.12;-1.35;-1.35;-1.35","2.24;2.24;.;.","0.948588;0.999995;0.948588","-2.38;-2.58;-2.71;-2.48","0.999;0.999;.;.","0.0;0.002;0.002;0.004","0.652;0.661;.;.",{"$nulls":3},"ExAC_NFE_AF",4.513e-05,{"$nulls":6},"C4747923| C4747940","0/0","435,0","0","435","0/1","295,32","0.0979","327",null,"chr8:108082626:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.097"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","RYR2","chr1:237506713","RYR2(V873M)",{"$nulls":6},255,"PASS","Missense","rs369248015",1.224889759921607E-4,"DISEASE: Arrhythmogenic right ventricular dysplasia, familial, 2 (ARVD2) [MIM:600996]: A congenital heart disease characterized by infiltration of adipose and fibrous tissue into the right ventricle and loss of myocardial cells, resulting in ventricular and supraventricular arrhythmias. {ECO:0000269|PubMed:11159936}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ventricular tachycardia, catecholaminergic polymorphic, 1, with or without atrial dysfunction and/or dilated cardiomyopathy (CPVT1) [MIM:604772]: An arrhythmogenic disorder characterized by stress-induced, bidirectional ventricular tachycardia that may degenerate into cardiac arrest and cause sudden death. Patients present with recurrent syncope, seizures, or sudden death after physical activity or emotional stress. CPVT1 inheritance is autosomal dominant. {ECO:0000269|PubMed:11157710, ECO:0000269|PubMed:11208676, ECO:0000269|PubMed:12093772, ECO:0000269|PubMed:12106942, ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:15046072, ECO:0000269|PubMed:15046073, ECO:0000269|PubMed:15466642, ECO:0000269|PubMed:15544015, ECO:0000269|PubMed:16188589, ECO:0000269|PubMed:17984046, ECO:0000269|PubMed:24793461, ECO:0000269|PubMed:25372681, ECO:0000269|PubMed:27733687}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering cardiac muscle contraction. Aberrant channel activation can lead to cardiac arrhythmia. In cardiac myocytes, calcium release is triggered by increased Ca(2+) levels due to activation of the L-type calcium channel CACNA1C. The calcium channel activity is modulated by formation of heterotetramers with RYR3. Required for cellular calcium ion homeostasis. Required for embryonic heart development. {ECO:0000269|PubMed:10830164, ECO:0000269|PubMed:20056922, ECO:0000269|PubMed:27733687}.; ","acmg",{"$nulls":3},"p.Val873Met","c.2617G>A","MODERATE","873/4967",23,{"$nulls":5},"4","580","506","511","434","416","363","0","0","0","0.2121",{"$nulls":20},"3.976391","-2.88;.","2.14;.","0.999141","-1.93;.","1.0;.","0.067;.","0.724;.",{"$nulls":3},"ESP6500_EA_AF",1.224889759921607E-4,"AD","Ventricular tachycardia, catecholaminergic polymorphic, 1; Arrhythmogenic right ventricular dysplasia 2  ","Cardiovascular",null,"This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008].  ",null,"C1832931| C4053736","0/0","558,0","0","558","0/1","397,93","0.1898","490",null,"chr1:237506713:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1935"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","SLC6A6","chr3:14468104","SLC6A6(G431R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Sodium-dependent taurine and beta-alanine transporter. Chloride ions are necessary for optimal uptake. {ECO:0000269|PubMed:8382624}.; ",{"$nulls":4},"p.Gly431Arg","c.1291G>A","MODERATE","431/721",9,{"$nulls":5},"5","635","404","466","285","565","359","0.0016","0.0016","0","0.2479",{"$nulls":20},"4.355761",null,"2.61;.","1",null,"0.983;.",null,"0.827;0.837",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","622,1","0.0016","623","0/1","291,91","0.2382","382",null,"chr3:14468104:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2316"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ST3GAL3","chr1:43920908","ST3GAL3(R409C)",{"$nulls":6},255,"PASS","Missense","rs1218848815",-1,"DISEASE: Mental retardation, autosomal recessive 12 (MRT12) [MIM:611090]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:21907012}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 15 (EIEE15) [MIM:615006]: A form of epilepsy that manifests in the neonatal or the early infantile period as severely impaired cognitive and motor development, due to recurrent clinical seizures or prominent interictal epileptiform discharges. Patients develop infantile spasms, mainly of the flexor type, between 3 and 7 months of age, which are accompanied by hypsarrhythmia on EEG. Other features include poor eye contact, hypotonia, primitive reflexes, and irritability. Seizures evolve clinically to Lennox-Gastaut syndrome. {ECO:0000269|PubMed:23252400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the formation of the NeuAc-alpha-2,3-Gal-beta- 1,4-GlcNAc-, NeuAc-alpha-2,3-Gal-beta-1,3-GlcNAc- and NeuAc-alpha- 2,3-Gal-beta-1,3-GalNAc- sequences found in terminal carbohydrate groups of glycoproteins and glycolipids. The highest activity is toward Gal-beta-1,3-GlcNAc and the lowest toward Gal-beta-1,3- GalNAc. {ECO:0000250|UniProtKB:P97325}.; ",{"$nulls":4},"p.Arg409Cys","c.1225C>T","MODERATE","409/444",12,{"$nulls":5},"5","528","465","330","315","479","409","0","0","0","0.1834",{"$nulls":20},"3.7483940000000002",".;1.5;1.5;1.5;.;.;.;.;.;.;1.5;.;.;.;.;1.5","1.46;.;.;.;.;.;.;.;1.46;.;.;.;.;1.46;.;.","0.999606;0.999499;0.999499;0.999499;0.999606;0.999499;0.999499;0.999499;0.999606;0.999606;0.999606;0.999606;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1",".;-0.98;-0.55;-1.01;.;.;.;.;.;.;-0.98;.;.;.;.;-0.97","0.997;0.998;0.999;0.998;.;.;0.997;0.998;0.997;.;0.998;.;.;0.997;.;0.997",".;0.015;0.023;0.017;.;.;.;.;.;.;0.139;.;.;.;.;0.035",".;0.449;0.448;0.45;.;.;.;.;.;.;0.429;.;.;.;.;0.444",{"$nulls":3},"Unknown",-1,"AR","Mental retardation, autosomal recessive 12; Epileptic encephalopathy, early infantile, 15","Neurologic",{"$nulls":3},"C3554316| C1970200","0/0","498,0","0","498","0/1","345,84","0.1958","429",null,"chr1:43920908:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1778"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","SYMPK","chr19:45821479","SYMPK(G933E)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing. Specific component of the tight junction (TJ) plaque, but might not be an exclusively junctional component. May have a house- keeping rule. Is involved in pre-mRNA polyadenylation. Enhances SSU72 phosphatase activity. {ECO:0000269|PubMed:16230528, ECO:0000269|PubMed:20861839}.; ",{"$nulls":4},"p.Gly933Glu","c.2798G>A","MODERATE","933/1274",22,{"$nulls":5},"5","375","288","257","196","358","272","0","0","0","0.0956",{"$nulls":20},"3.625022","-0.23;.;.","1.9;.;.","0.999993","-1.37;.;.","0.445;.;.","0.079;.;.","0.717;0.617;0.615",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","368,0","0","368","0/1","250,26","0.0942","276",null,"chr19:45821479:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0918"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","SYN2","chr3:12004744","SYN2(A65T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:15449241}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; ","FUNCTION: Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. May play a role in noradrenaline secretion by sympathetic neurons (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ala65Thr","c.193G>A","MODERATE","65/582",1,{"$nulls":5},"4","69","34","59","27",null,null,"0","0",{"$nulls":22},"1.5564900000000002",null,null,"0.999981",{"$nulls":3},"0.29;0.292",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014].",null,"C0036341","0/0","68,0","0","68","0/1","21,10","0.3226","31",null,"chr3:12004744:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2593"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TACC2","chr10:122083317","TACC2(P273S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors (By similarity). May play a role in organizing centrosomal microtubules. May act as a tumor suppressor protein. May represent a tumor progression marker. {ECO:0000250, ECO:0000269|PubMed:10749935}.; ",{"$nulls":4},"p.Pro273Ser","c.817C>T","MODERATE","273/2948",3,{"$nulls":5},"5","432","378","321","276","375","328","0","0","0","0.1585",{"$nulls":20},"1.012339","4.09;4.04;4.05;4.09;4.04","1.04;.;.;1.04;.","1","-1.0;-0.96;-0.79;-1.0;-0.96","0.728","0.138;0.15;0.157;0.138;0.15","0.081;0.091;0.134;0.085;0.119",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","427,0","0","427","0/1","308,63","0.1698","371",null,"chr10:122083317:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1594"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TACC2","chr10:122087304","TACC2(E1602K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors (By similarity). May play a role in organizing centrosomal microtubules. May act as a tumor suppressor protein. May represent a tumor progression marker. {ECO:0000250, ECO:0000269|PubMed:10749935}.; ",{"$nulls":4},"p.Glu1602Lys","c.4804G>A","MODERATE","1602/2948",3,{"$nulls":5},"5","633","431","508","363","494","361","0","0","0","0.2438",{"$nulls":20},"2.595652","3.49;3.57;3.42;3.49;3.57","1.75;.;.;1.75;.","0.554652;0.554652;1;1;1;1;1","-0.71;-0.84;-0.68;-0.71;-0.84","0.99","0.005;0.004;0.005;0.005;0.004","0.183;0.131;0.238;0.178;0.114",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","618,0","0","618","0/1","320,106","0.2488","426",null,"chr10:122087304:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2452"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TCF3","chr19:1622175","TCF3(A263V)",{"$nulls":6},255,"PASS","Missense","rs756170287",8.582999999999999E-6,"DISEASE: Note=Chromosomal aberrations involving TCF3 are cause of forms of pre-B-cell acute lymphoblastic leukemia (B-ALL). Translocation t(1;19)(q23;p13.3) with PBX1. TCF3-PBX1 transforms cells by constitutively activating transcription of genes regulated by PBX1 or by other members of the PBX protein family (PubMed:1967983, PubMed:1671560). Translocation t(17;19)(q22;p13.3) with HLF (PubMed:1386162). Inversion inv(19)(p13;q13) with TFPT (PubMed:10086727). {ECO:0000269|PubMed:10086727, ECO:0000269|PubMed:1386162, ECO:0000269|PubMed:1671560, ECO:0000269|PubMed:1967983}.; DISEASE: Agammaglobulinemia 8, autosomal dominant (AGM8) [MIM:616941]: A form of agammaglobulinemia, a primary immunodeficiency characterized by profoundly low or absent serum antibodies and low or absent circulating B-cells due to an early block of B-cell development. Affected individuals develop severe infections in the first years of life. {ECO:0000269|PubMed:24216514}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transcriptional regulator. Involved in the initiation of neuronal differentiation. Heterodimers between TCF3 and tissue- specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E- box motifs: 5'-CANNTG-3'. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. Binds to IEB1 and IEB2, which are short DNA sequences in the insulin gene transcription control region. {ECO:0000250|UniProtKB:P15806}.; ","gedi|level2",{"$nulls":3},"p.Ala263Val","c.788C>T","MODERATE","263/679",10,{"$nulls":5},"5","185","193","144","158","156","167","0","0","0","0.1078",{"$nulls":20},"1.005609","0.92;.;.;.;0.92;0.92","1.87;.;1.87;.;1.87;.","1","-1.91;.;.;.;.;-1.68","0.063;.;0.063;.;0.153;.","0.188;.;.;.;.;0.223","0.057;0.079;0.057;0.074;0.058;0.082",{"$nulls":3},"ExAC_AF",8.582999999999999E-6,{"$nulls":3},"COSMIC",null,null,"C4310786","0/0","177,0","0","177","0/1","159,23","0.1264","182",null,"chr19:1622175:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1392"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TDRD9","chr14:103991194","TDRD9(E384K)",null,null,"domain (Helicase C-terminal )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Defects in TDRD9 may be a cause of non-obstructive azoospermia, a disorder characterized by the absence of sperm. Female fertility is not affected. {ECO:0000269|PubMed:28536242}.; ","FUNCTION: ATP-binding RNA helicase required during spermatogenesis (PubMed:28536242). Required to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Acts downstream of piRNA biogenesis: exclusively required for transposon silencing in the nucleus, suggesting that it acts as a nuclear effector in the nucleus together with PIWIL4. {ECO:0000250|UniProtKB:Q14BI7, ECO:0000269|PubMed:28536242}.; ",{"$nulls":4},"p.Glu384Lys","c.1150G>A","MODERATE","384/1382",9,{"$nulls":5},"5","714","594","498","392","664","527","0","0","0","0.1841",{"$nulls":20},"2.469122","4.24;.","1.485;.","1","-1.62;.","0.155;.","0.087;.","0.413;0.488",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748224","0/0","685,0","0","685","0/1","423,115","0.2138","538",null,"chr14:103991194:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2066"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TMEM132C","chr12:128705501","TMEM132C(P845S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro845Ser","c.2533C>T","MODERATE","845/1108",9,1,{"$nulls":4},"4","759","502","592","382","665","432","0","0","0","0.2338",{"$nulls":20},"-0.949233","3.89","-1.265","1","0.49","0.002","0.724","0.016",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","750,0","0","750","0/1","371,116","0.2382","487",null,"chr12:128705501:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.233"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TP53","chr17:7673803","TP53(R234C)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234C)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234D)), sequence variant (In a sporadic cancer; somatic mutation. TP53(Y234F)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234H)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234N)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234Q)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234S)), strand ",{"$nulls":3},255,"PASS","Missense","rs121913343",1.605E-5,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg234Cys","c.700C>T","MODERATE","234/410",8,968,{"$nulls":4},"5","294","197","223","145","261","177","0","0","0","0.1921",{"$nulls":20},"4.3774","-7.34;.;.;.;.;.;.;.;-7.34;.;.;-7.34;-7.34;.;.;-7.34;.;.;-7.34",".;.;.;.;.;.;.;.;3.18;.;3.18;3.18;3.18;.;.;3.18;.;.;.","1","-7.38;.;.;.;.;.;.;.;-7.65;.;.;-7.38;-7.38;.;.;-7.65;.;.;-6.91",".;.;.;.;.;.;.;.;1.0;.;1.0;1.0;1.0;.;.;1.0;.;.;.","0.002;.;.;.;.;.;.;.;0.002;.;.;0.002;0.002;.;.;0.002;.;.;0.003","0.954;0.943;0.953;0.954;0.903;0.954;0.937;0.97;0.971;0.97;0.955;0.955;0.955;0.954;0.913;0.973;0.97;0.956;.",{"$nulls":3},"ExAC_NFE_AF",1.605E-5,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","292,0","0","292","0/1","151,42","0.2176","193",null,"chr17:7673803:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2276"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TRIM17","chr1:228408265","TRIM17(C457Y)",null,null,"domain (B30.2/SPRY ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as a ubiquitin E3 ligase. {ECO:0000269|PubMed:19358823}.; ",{"$nulls":4},"p.Cys457Tyr","c.1370G>A","MODERATE","457/477",7,{"$nulls":5},"5","351","486","293","396","249","395","0","0","0","0.1772",{"$nulls":20},"2.292895","-0.29","0.615","0.99529","0.47","0.999","0.767","0.213;0.215;0.216",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","342,0","0","342","0/1","395,72","0.1542","467",null,"chr1:228408265:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1616"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TRPV1","chr17:3573791","TRPV1(E660K)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Ligand-activated non-selective calcium permeant cation channel involved in detection of noxious chemical and thermal stimuli. Seems to mediate proton influx and may be involved in intracellular acidosis in nociceptive neurons. Involved in mediation of inflammatory pain and hyperalgesia. Sensitized by a phosphatidylinositol second messenger system activated by receptor tyrosine kinases, which involves PKC isozymes and PCL. Activation by vanilloids, like capsaicin, and temperatures higher than 42 degrees Celsius, exhibits a time- and Ca(2+)-dependent outward rectification, followed by a long-lasting refractory state. Mild extracellular acidic pH (6.5) potentiates channel activation by noxious heat and vanilloids, whereas acidic conditions (pH <6) directly activate the channel. Can be activated by endogenous compounds, including 12-hydroperoxytetraenoic acid and bradykinin. Acts as ionotropic endocannabinoid receptor with central neuromodulatory effects. Triggers a form of long-term depression (TRPV1-LTD) mediated by the endocannabinoid anandamine in the hippocampus and nucleus accumbens by affecting AMPA receptors endocytosis. {ECO:0000250|UniProtKB:O35433, ECO:0000269|PubMed:11050376, ECO:0000269|PubMed:11226139, ECO:0000269|PubMed:11243859, ECO:0000269|PubMed:12077606}.; ",{"$nulls":4},"p.Glu660Lys","c.1978G>A","MODERATE","660/850",13,{"$nulls":5},"5","946","657","741","515","799","565","0","0","0","0.2248",{"$nulls":20},"3.318647","-1.93","2.65;2.65;2.65;2.65;.;.;.","1","-3.08;.;.;-3.08;-3.08;.;-3.11","0.083;0.083;0.083;0.083;0.146;.;0.138","0.014;.;.;0.014;0.007;.;0.01","0.824;0.839;0.84;0.824;0.776;0.842;0.825",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","939,0","0","939","0/1","497,144","0.2246","641",null,"chr17:3573791:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2369"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TSSK2","chr22:19131727","TSSK2(E110K)",null,null,"domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Testis-specific serine/threonine-protein kinase required during spermatid development. Phosphorylates TSKS at 'Ser-288' and SPAG16. Involved in the late stages of spermatogenesis, during the reconstruction of the cytoplasm. During spermatogenesis, required for the transformation of a ring-shaped structure around the base of the flagellum originating from the chromatoid body. {ECO:0000269|PubMed:15044604, ECO:0000269|PubMed:18533145, ECO:0000269|PubMed:20729278}.; ",{"$nulls":4},"p.Glu110Lys","c.328G>A","MODERATE","110/358",1,{"$nulls":5},"5","726","604","564","477","656","529","0","0","0","0.0888",{"$nulls":20},"3.848822","-1.92","2.355","1;0.548347","-3.77","0.995","0.002","0.772",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","714,0","0","714","0/1","539,55","0.0926","594",null,"chr22:19131727:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0901"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","TYROBP","chr19:35907531","TYROBP(M48I)",null,null,"transmembrane region (Helical ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL) [MIM:221770]: Recessively inherited disease characterized by a combination of psychotic symptoms rapidly progressing to presenile dementia and bone cysts restricted to wrists and ankles. PLOSL has a global distribution, although most of the patients have been diagnosed in Finland and Japan, with an estimated population prevalence of 2x10(-6) in the Finns. {ECO:0000269|PubMed:10888890, ECO:0000269|PubMed:12370476}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Non-covalently associates with activating receptors of the CD300 family. Cross-linking of CD300-TYROBP complexes results in cellular activation. Involved for instance in neutrophil activation mediated by integrin.; ",{"$nulls":4},"p.Met48Ile","c.144G>A","MODERATE","48/144",3,{"$nulls":5},"5","387","334","306","266","358","296","0","0","0","0.0946",{"$nulls":20},"1.040197","-1.87",".;.;.;0;0","0.999983;0.999813;0.999813;0.999813;0.999983",".;.;1.01;0.97;.",".;.;.;0.01;0.01",".;.;0.202;0.29;.","0.289;0.292;0.298;0.283;0.272",{"$nulls":3},"Unknown",-1,"AR","Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy; Nasu-Hakola disease ","Musculoskeletal; Neurologic",{"$nulls":3},"C4721893","0/0","386,0","0","386","0/1","288,37","0.1138","325",null,"chr19:35907531:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1015"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","UGT2B11","chr4:69200663","UGT2B11(P456L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds.; ",{"$nulls":4},"p.Pro456Leu","c.1367C>T","MODERATE","456/529",6,{"$nulls":5},"3",null,null,"503","392","704","462",null,null,"0","0.0563",{"$nulls":20},"3.175737","-0.99","4.355","0.945407","-9.21","1.0",null,"0.436",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","698,0","0","698","0/1","490,36","0.0684","526",null,"chr4:69200663:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0765"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","USH2A","chr1:215674167","USH2A(I4582L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Usher syndrome 2A (USH2A) [MIM:276901]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH2 is characterized by congenital mild hearing impairment with normal vestibular responses. {ECO:0000269|PubMed:10729113, ECO:0000269|PubMed:10738000, ECO:0000269|PubMed:10909849, ECO:0000269|PubMed:11311042, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12525556, ECO:0000269|PubMed:14970843, ECO:0000269|PubMed:15015129, ECO:0000269|PubMed:15025721, ECO:0000269|PubMed:15241801, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17405132, ECO:0000269|PubMed:18273898, ECO:0000269|PubMed:18452394, ECO:0000269|PubMed:19683999, ECO:0000269|PubMed:19737284, ECO:0000269|PubMed:20309401, ECO:0000269|PubMed:20440071, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21593743, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22004887, ECO:0000269|PubMed:23737954, ECO:0000269|PubMed:26377068, ECO:0000269|PubMed:9624053}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in USH2A has been found in a patient with a form of non-syndromic sensorineural hearing loss. {ECO:0000269|PubMed:25388789}.; ","FUNCTION: Involved in hearing and vision.; ",{"$nulls":4},"p.Ile4582Leu","c.13744A>T","MODERATE","4582/5202",63,{"$nulls":5},"5","429","414","309","319","384","358","0","0","0","0.0922",{"$nulls":20},"0.601862","0.46","0.965","1","-0.34","0.003","0.309","0.114",{"$nulls":3},"Unknown",-1,"AR","Usher syndrome, type 2A","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008].",null,"C3151138| C1848634","0/0","425,0","0","425","0/1","371,38","0.0929","409",null,"chr1:215674167:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1003"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ZNF16","chr8:144931226","ZNF16(E521K)",null,null,"zinc finger region (C2H2-type 12 )",{"$nulls":3},255,"PASS","Missense","rs141655692",1.499E-5,null,"FUNCTION: Acts as a transcriptional activator. Promotes cell proliferation by facilitating the cell cycle phase transition from the S to G2/M phase. Involved in both the hemin- and phorbol myristate acetate (PMA)-induced erythroid and megakaryocytic differentiation, respectively. Plays also a role as an inhibitor of cell apoptosis. {ECO:0000269|PubMed:16628192, ECO:0000269|PubMed:19763908, ECO:0000269|PubMed:21874239}.; ",{"$nulls":4},"p.Glu521Lys","c.1561G>A","MODERATE","521/682",4,{"$nulls":5},"5","291","298","246","231","192","203","0","0","0","0.0887",{"$nulls":20},"2.355123","2.33;.;2.33","0.165","0.999129","-3.49;.;-3.49","1.0","0.036;.;0.036","0.376;0.372;0.377",{"$nulls":3},"ExAC_NFE_AF",1.499E-5,{"$nulls":7},"0/0","293,0","0","293","0/1","259,26","0.0912","285",null,"chr8:144931226:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0952"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ZNF30","chr19:34931918","ZNF30(E29K)",null,null,"domain (KRAB )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu29Lys","c.85G>A","MODERATE","29/624",3,{"$nulls":5},"4","719","527","507","387","639","459","0","0","0","0.1634",{"$nulls":20},"1.211348","4.59;4.59;.;4.59;4.59","1.015;1.015;.;1.015;1.015","1;0.999418;0.999418","-1.69;-1.69;.;.;.","0.0;0.0;.;.;0.822","0.586;0.493;.;.;.","0.245;0.231;.;0.177;0.246",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","698,0","0","698","0/1","425,91","0.1764","516",null,"chr19:34931918:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.186"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ZNF418","chr19:57932485","ZNF418(G4D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional repressor. {ECO:0000269|Ref.1}.; ",{"$nulls":4},"p.Gly4Asp","c.11G>A","MODERATE","4/697",3,{"$nulls":5},"5","388","294","242","193","367","267","0","0","0","0.161",{"$nulls":20},"0.635198","3.06;2.1",null,"1","-1.16;.",null,"0.498;.","0.175;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","384,0","0","384","0/1","235,46","0.1637","281",null,"chr19:57932485:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1503"]
["09JM","T10","JLPIKTOR_JLPIKTOR_17113009JM","ZNF763","chr19:11978135","ZNF763(V74F)",{"$nulls":3},"antibody-mapping:heterologous_protein_expression_evidence","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Val74Phe","c.220G>T","MODERATE","74/397",4,1,{"$nulls":4},"5","382","242","311","208","328","204","0","0","0","0.1912",{"$nulls":20},"0.48376","3.39;3.37;3.37;5.17",".;.;-0.305;.","1;1;1;1;0.999999",".;-1.07;-1.03;.",".;0.014;0.998;.",".;0.167;0.167;.","0.124;0.109;0.129;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","375,0","0","375","0/1","196,48","0.1967","244",null,"chr19:11978135:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113009JM","somatic","somatic","JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113009JM/somatic/JLPIKTOR_17113009JM_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113009JM_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1971"]

{"sheet":"10LD","index":7,"n_rows":427,"n_cols":107,"rows_kept":427}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AASS","chr7:122086148","AASS(L683P)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hyperlysinemia, 1 (HYPLYS1) [MIM:238700]: An autosomal recessive metabolic condition with variable clinical features. Some patients present with non-specific seizures, hypotonia, or mildly delayed psychomotor development, and increased serum lysine and pipecolic acid on laboratory analysis. However, about half of the probands are reported to be asymptomatic, and hyperlysinemia is generally considered to be a benign metabolic variant. {ECO:0000269|PubMed:10775527}. Note=The disease is caused by mutations affecting the gene represented in this entry. In hyperlysinemia 1, both enzymatic functions of AASS are defective and patients have increased serum lysine and possibly increased saccharopine. Some individuals, however, retain significant amounts of lysine-ketoglutarate reductase and present with saccharopinuria, a metabolic condition with few, if any, clinical manifestations. {ECO:0000305|PubMed:463877}.; DISEASE: 2,4-dienoyl-CoA reductase deficiency (DECRD) [MIM:616034]: A rare, autosomal recessive, inborn error of polyunsaturated fatty acids and lysine metabolism, resulting in mitochondrial dysfunction. Affected individuals have a severe encephalopathy with neurologic and metabolic abnormalities beginning in early infancy. Laboratory studies show increased C10:2 carnitine levels and hyperlysinemia. {ECO:0000269|PubMed:24847004}. Note=The protein represented in this entry is involved in disease pathogenesis. A selective decrease in mitochondrial NADP(H) levels due to NADK2 mutations causes a deficiency of NADPH-dependent mitochondrial enzymes, such as DECR1 and AASS. {ECO:0000269|PubMed:24847004}.; ","FUNCTION: Bifunctional enzyme that catalyzes the first two steps in lysine degradation. The N-terminal and the C-terminal contain lysine-ketoglutarate reductase and saccharopine dehydrogenase activity, respectively.; ","mitocarta",{"$nulls":3},"p.Leu683Pro","c.2048T>C","MODERATE","683/926",18,{"$nulls":5},"5","195","257","134","167","184","225","0","0","0","0.2311",{"$nulls":20},"3.041028","0.97","2.485","1","-3.97","0.12","0.003","0.81;0.809",{"$nulls":3},"Unknown",-1,"AR","Hyperlysinemia","Biochemical",{"$nulls":3},"C0543533","0/0","195,0","0","195","0/1","188,62","0.248","250",null,"chr7:122086148:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2335"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","AASS","chr7:122086148","AASS(L683P)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hyperlysinemia, 1 (HYPLYS1) [MIM:238700]: An autosomal recessive metabolic condition with variable clinical features. Some patients present with non-specific seizures, hypotonia, or mildly delayed psychomotor development, and increased serum lysine and pipecolic acid on laboratory analysis. However, about half of the probands are reported to be asymptomatic, and hyperlysinemia is generally considered to be a benign metabolic variant. {ECO:0000269|PubMed:10775527}. Note=The disease is caused by mutations affecting the gene represented in this entry. In hyperlysinemia 1, both enzymatic functions of AASS are defective and patients have increased serum lysine and possibly increased saccharopine. Some individuals, however, retain significant amounts of lysine-ketoglutarate reductase and present with saccharopinuria, a metabolic condition with few, if any, clinical manifestations. {ECO:0000305|PubMed:463877}.; DISEASE: 2,4-dienoyl-CoA reductase deficiency (DECRD) [MIM:616034]: A rare, autosomal recessive, inborn error of polyunsaturated fatty acids and lysine metabolism, resulting in mitochondrial dysfunction. Affected individuals have a severe encephalopathy with neurologic and metabolic abnormalities beginning in early infancy. Laboratory studies show increased C10:2 carnitine levels and hyperlysinemia. {ECO:0000269|PubMed:24847004}. Note=The protein represented in this entry is involved in disease pathogenesis. A selective decrease in mitochondrial NADP(H) levels due to NADK2 mutations causes a deficiency of NADPH-dependent mitochondrial enzymes, such as DECR1 and AASS. {ECO:0000269|PubMed:24847004}.; ","FUNCTION: Bifunctional enzyme that catalyzes the first two steps in lysine degradation. The N-terminal and the C-terminal contain lysine-ketoglutarate reductase and saccharopine dehydrogenase activity, respectively.; ","mitocarta",{"$nulls":3},"p.Leu683Pro","c.2048T>C","MODERATE","683/926",18,{"$nulls":5},"5","195","118","134","83","184","108","0","0","0","0.5556",{"$nulls":20},"3.041028","0.97","2.485","1","-3.97","0.12","0.003","0.81;0.809",{"$nulls":3},"Unknown",-1,"AR","Hyperlysinemia","Biochemical",{"$nulls":3},"C0543533","0/0","195,0","0","195","0/1","47,61","0.5648","108",null,"chr7:122086148:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5181"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABCA7","chr19:1055257","ABCA7(A1371T)",{"$nulls":6},255,"PASS","Missense","rs1437780552",-1,"DISEASE: Alzheimer disease 9 (AD9) [MIM:608907]: A familial, late- onset form of Alzheimer disease. Alzheimer disease is a neurodegenerative disorder characterized by progressive dementia, loss of cognitive abilities, and deposition of fibrillar amyloid proteins as intraneuronal neurofibrillary tangles, extracellular amyloid plaques and vascular amyloid deposits. The major constituents of these plaques are neurotoxic amyloid-beta protein 40 and amyloid-beta protein 42, that are produced by the proteolysis of the transmembrane APP protein. The cytotoxic C- terminal fragments (CTFs) and the caspase-cleaved products, such as C31, are also implicated in neuronal death. {ECO:0000269|PubMed:25807283, ECO:0000269|PubMed:26141617}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in phagocytosis by macrophages of apoptotic cells. Binds APOA1 and may function in apolipoprotein-mediated phospholipid efflux from cells. May also mediate cholesterol efflux. May regulate cellular ceramide homeostasis during keratinocytes differentiation. {ECO:0000269|PubMed:12917409, ECO:0000269|PubMed:12925201, ECO:0000269|PubMed:14570867, ECO:0000269|PubMed:14592415}.; ",{"$nulls":4},"p.Ala1371Thr","c.4111G>A","MODERATE","1371/2146",30,{"$nulls":5},"5","325","312","239","214","292","267","0","0","0","0.1386",{"$nulls":20},"1.522236","-3.49","2.3;2.3;.","0.792481;0.750088;0.792481","-0.77;-0.77;.","0.865;0.865;0.868","0.13;0.13;.","0.239;0.259;0.164",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4282179","0/0","317,0","0","317","0/1","257,39","0.1318","296",null,"chr19:1055257:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1402"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABCB6","chr2:219218199","ABCB6(A159P)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Microphthalmia, isolated, with coloboma, 7 (MCOPCB7) [MIM:614497]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269|PubMed:22226084}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dyschromatosis universalis hereditaria 3 (DUH3) [MIM:615402]: An autosomal dominant pigmentary genodermatosis characterized by a mixture of hyperpigmented and hypopigmented macules distributed randomly over the body, that appear in infancy or early childhood. The trunk and extremities are the dominant sites of abnormal pigmentation. Facial lesions can be seen in 50% of affected individuals, but involvement of palms and soles is unusual. Abnormalities of hair and nails have also been reported. Dyschromatosis universalis hereditaria may be associated with abnormalities of dermal connective tissue, nerve tissue, or other systemic complications. {ECO:0000269|PubMed:23519333, ECO:0000269|PubMed:24224009, ECO:0000269|PubMed:24498303, ECO:0000269|PubMed:25288164}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pseudohyperkalemia, familial, 2, due to red cell leak (PSHK2) [MIM:609153]: A dominantly inherited condition characterized by increased serum potassium levels, measured in whole-blood specimens stored at or below room temperature. This condition is not accompanied by clinical symptoms or biological signs except for borderline abnormalities of red cell shape. {ECO:0000269|PubMed:23180570, ECO:0000269|PubMed:24947683}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds heme and porphyrins and functions in their ATP- dependent uptake into the mitochondria. Plays a crucial role in heme synthesis. {ECO:0000269|PubMed:10837493, ECO:0000269|PubMed:17006453}.; ","mitocarta",{"$nulls":3},"p.Ala159Pro","c.475G>C","MODERATE","159/842",1,{"$nulls":5},"5","584","672","441","497","467","549","0","0","0","0.1311",{"$nulls":20},"2.3370480000000002","-1.55;.","1.955","0.999975","-2.41;.","0.574;0.654","0.085;.","0.629;.",{"$nulls":3},"Unknown",-1,"BG","Blood group, Langereis system","Dermatologic; Hematologic; Ophthalmologic",{"$nulls":3},"C3809394| C1836705| C3281027| C3276339","0/0","578,0","0","578","0/1","572,89","0.1346","661",null,"chr2:219218199:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1288"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABCB6","chr2:219218199","ABCB6(A159P)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Microphthalmia, isolated, with coloboma, 7 (MCOPCB7) [MIM:614497]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269|PubMed:22226084}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dyschromatosis universalis hereditaria 3 (DUH3) [MIM:615402]: An autosomal dominant pigmentary genodermatosis characterized by a mixture of hyperpigmented and hypopigmented macules distributed randomly over the body, that appear in infancy or early childhood. The trunk and extremities are the dominant sites of abnormal pigmentation. Facial lesions can be seen in 50% of affected individuals, but involvement of palms and soles is unusual. Abnormalities of hair and nails have also been reported. Dyschromatosis universalis hereditaria may be associated with abnormalities of dermal connective tissue, nerve tissue, or other systemic complications. {ECO:0000269|PubMed:23519333, ECO:0000269|PubMed:24224009, ECO:0000269|PubMed:24498303, ECO:0000269|PubMed:25288164}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pseudohyperkalemia, familial, 2, due to red cell leak (PSHK2) [MIM:609153]: A dominantly inherited condition characterized by increased serum potassium levels, measured in whole-blood specimens stored at or below room temperature. This condition is not accompanied by clinical symptoms or biological signs except for borderline abnormalities of red cell shape. {ECO:0000269|PubMed:23180570, ECO:0000269|PubMed:24947683}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds heme and porphyrins and functions in their ATP- dependent uptake into the mitochondria. Plays a crucial role in heme synthesis. {ECO:0000269|PubMed:10837493, ECO:0000269|PubMed:17006453}.; ","mitocarta",{"$nulls":3},"p.Ala159Pro","c.475G>C","MODERATE","159/842",1,{"$nulls":5},"5","584","305","441","243","466","260","0","0","0","0.2923",{"$nulls":20},"2.3370480000000002","-1.55;.","1.955","0.999975","-2.41;.","0.574;0.654","0.085;.","0.629;.",{"$nulls":3},"Unknown",-1,"BG","Blood group, Langereis system","Dermatologic; Hematologic; Ophthalmologic",{"$nulls":3},"C3809394| C1836705| C3281027| C3276339","0/0","576,0","0","576","0/1","219,85","0.2796","304",null,"chr2:219218199:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2798"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABCB7","chrX:75071647","ABCB7(D358N)",null,null,"domain (ABC transmembrane type-1 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Anemia, sideroblastic, spinocerebellar ataxia (ASAT) [MIM:301310]: A X-linked recessive disorder characterized by an infantile to early childhood onset of non-progressive cerebellar ataxia and mild anemia, with hypochromia and microcytosis. {ECO:0000269|PubMed:10196363, ECO:0000269|PubMed:11050011, ECO:0000269|PubMed:11843825, ECO:0000269|PubMed:22398176}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Could be involved in the transport of heme from the mitochondria to the cytosol. Plays a central role in the maturation of cytosolic iron-sulfur (Fe/S) cluster-containing proteins.; ","mito100",{"$nulls":3},"p.Asp358Asn","c.1072G>A","MODERATE","358/753",9,{"$nulls":5},"4","164","150","105","89","155","135","0","0","0","0.2148",{"$nulls":20},"3.533252",".;-2.5;.;-2.5;-2.5;.;-2.5",".;.;.;.;1.92;.;.","1",".;-3.93;.;-3.93;-3.93;.;-3.93","0.983;0.983;.;.;0.096;.;.",".;0.146;.;0.157;0.141;.;0.103",".;0.692;.;0.706;0.695;0.708;.",{"$nulls":3},"Unknown",-1,"XL","Anemia, sideroblastic, and spinocerebellar ataxia","Hematologic; Neurologic",{"$nulls":3},"C1845028","0/0","158,0","0","158","0/1","110,35","0.2414","145",null,"chrX:75071647:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2247"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABCB7","chrX:75071647","ABCB7(D358N)",null,null,"domain (ABC transmembrane type-1 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Anemia, sideroblastic, spinocerebellar ataxia (ASAT) [MIM:301310]: A X-linked recessive disorder characterized by an infantile to early childhood onset of non-progressive cerebellar ataxia and mild anemia, with hypochromia and microcytosis. {ECO:0000269|PubMed:10196363, ECO:0000269|PubMed:11050011, ECO:0000269|PubMed:11843825, ECO:0000269|PubMed:22398176}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Could be involved in the transport of heme from the mitochondria to the cytosol. Plays a central role in the maturation of cytosolic iron-sulfur (Fe/S) cluster-containing proteins.; ","mito100",{"$nulls":3},"p.Asp358Asn","c.1072G>A","MODERATE","358/753",9,{"$nulls":5},"4","164","92","105","58","152","83","0","0","0","0.3373",{"$nulls":20},"3.533252",".;-2.5;.;-2.5;-2.5;.;-2.5",".;.;.;.;1.92;.;.","1",".;-3.93;.;-3.93;-3.93;.;-3.93","0.983;0.983;.;.;0.096;.;.",".;0.146;.;0.157;0.141;.;0.103",".;0.692;.;0.706;0.695;0.708;.",{"$nulls":3},"Unknown",-1,"XL","Anemia, sideroblastic, and spinocerebellar ataxia","Hematologic; Neurologic",{"$nulls":3},"C1845028","0/0","157,0","0","157","0/1","57,33","0.3667","90",null,"chrX:75071647:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3966"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABCC8","chr11:17394362","ABCC8(Q1484H)",null,null,"topological domain (Cytoplasmic ), domain (ABC transporter 2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Leucine-induced hypoglycemia (LIH) [MIM:240800]: Rare cause of hypoglycemia and is described as a condition in which symptomatic hypoglycemia is provoked by high protein feedings. Hypoglycemia is also elicited by administration of oral or intravenous infusions of a single amino acid, leucine. {ECO:0000269|PubMed:15356046}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Familial hyperinsulinemic hypoglycemia 1 (HHF1) [MIM:256450]: Most common cause of persistent hypoglycemia in infancy. Unless early and aggressive intervention is undertaken, brain damage from recurrent episodes of hypoglycemia may occur. {ECO:0000269|PubMed:10202168, ECO:0000269|PubMed:10334322, ECO:0000269|PubMed:10615958, ECO:0000269|PubMed:11018078, ECO:0000269|PubMed:11226335, ECO:0000269|PubMed:11867634, ECO:0000269|PubMed:12364426, ECO:0000269|PubMed:12941782, ECO:0000269|PubMed:15562009, ECO:0000269|PubMed:15579781, ECO:0000269|PubMed:15807877, ECO:0000269|PubMed:16357843, ECO:0000269|PubMed:16429405, ECO:0000269|PubMed:24814349, ECO:0000269|PubMed:25720052, ECO:0000269|PubMed:8650576, ECO:0000269|PubMed:8751851, ECO:0000269|PubMed:8923011, ECO:0000269|PubMed:9618169, ECO:0000269|PubMed:9648840, ECO:0000269|PubMed:9769320}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Diabetes mellitus, permanent neonatal (PNDM) [MIM:606176]: A rare form of diabetes distinct from childhood- onset autoimmune diabetes mellitus type 1. It is characterized by insulin-requiring hyperglycemia that is diagnosed within the first months of life. Permanent neonatal diabetes requires lifelong therapy. {ECO:0000269|PubMed:16613899, ECO:0000269|PubMed:16885549, ECO:0000269|PubMed:17213273, ECO:0000269|PubMed:17668386}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Transient neonatal diabetes mellitus 2 (TNDM2) [MIM:610374]: Neonatal diabetes is a form of diabetes mellitus defined by the onset of mild-to-severe hyperglycemia within the first months of life. Transient neonatal diabetes remits early, with a possible relapse during adolescence. {ECO:0000269|PubMed:16885549}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Subunit of the beta-cell ATP-sensitive potassium channel (KATP). Regulator of ATP-sensitive K(+) channels and insulin release. {ECO:0000269|PubMed:24814349, ECO:0000269|PubMed:25720052}.; ",{"$nulls":4},"p.Gln1484His","c.4452G>C","MODERATE","1484/1582",37,{"$nulls":5},"4","1028","1187","787","895","899","1003","0","0","0","0.2732",{"$nulls":20},"2.538955",".;.;-3.34;-3.34;.;.;.;.",".;.;1.02;.;.;.;.;.","0.999866",".;.;-1.71;-1.71;.;.;.;.",".;.;0.404;.;.;.;.;.",".;.;0.002;0.002;.;.;.;.",".;.;0.502;0.508;.;.;.;.",{"$nulls":3},"Unknown",-1,"AD/AR","Diabetes mellitus, transient neonatal, 2; Diabetes, permanent neonatal; Hyperinsulinemic hypoglycemia, familial, 1; Hypoglycemia, leucine-induced","Endocrine",{"$nulls":3},"C0271714| CN280869| C1835887| C0011860| C2931832| C1833104","0/0","999,0","0","999","0/1","815,320","0.2819","1135",null,"chr11:17394362:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.276"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABCC8","chr11:17394362","ABCC8(Q1484H)",null,null,"topological domain (Cytoplasmic ), domain (ABC transporter 2 ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Leucine-induced hypoglycemia (LIH) [MIM:240800]: Rare cause of hypoglycemia and is described as a condition in which symptomatic hypoglycemia is provoked by high protein feedings. Hypoglycemia is also elicited by administration of oral or intravenous infusions of a single amino acid, leucine. {ECO:0000269|PubMed:15356046}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Familial hyperinsulinemic hypoglycemia 1 (HHF1) [MIM:256450]: Most common cause of persistent hypoglycemia in infancy. Unless early and aggressive intervention is undertaken, brain damage from recurrent episodes of hypoglycemia may occur. {ECO:0000269|PubMed:10202168, ECO:0000269|PubMed:10334322, ECO:0000269|PubMed:10615958, ECO:0000269|PubMed:11018078, ECO:0000269|PubMed:11226335, ECO:0000269|PubMed:11867634, ECO:0000269|PubMed:12364426, ECO:0000269|PubMed:12941782, ECO:0000269|PubMed:15562009, ECO:0000269|PubMed:15579781, ECO:0000269|PubMed:15807877, ECO:0000269|PubMed:16357843, ECO:0000269|PubMed:16429405, ECO:0000269|PubMed:24814349, ECO:0000269|PubMed:25720052, ECO:0000269|PubMed:8650576, ECO:0000269|PubMed:8751851, ECO:0000269|PubMed:8923011, ECO:0000269|PubMed:9618169, ECO:0000269|PubMed:9648840, ECO:0000269|PubMed:9769320}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Diabetes mellitus, permanent neonatal (PNDM) [MIM:606176]: A rare form of diabetes distinct from childhood- onset autoimmune diabetes mellitus type 1. It is characterized by insulin-requiring hyperglycemia that is diagnosed within the first months of life. Permanent neonatal diabetes requires lifelong therapy. {ECO:0000269|PubMed:16613899, ECO:0000269|PubMed:16885549, ECO:0000269|PubMed:17213273, ECO:0000269|PubMed:17668386}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Transient neonatal diabetes mellitus 2 (TNDM2) [MIM:610374]: Neonatal diabetes is a form of diabetes mellitus defined by the onset of mild-to-severe hyperglycemia within the first months of life. Transient neonatal diabetes remits early, with a possible relapse during adolescence. {ECO:0000269|PubMed:16885549}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Subunit of the beta-cell ATP-sensitive potassium channel (KATP). Regulator of ATP-sensitive K(+) channels and insulin release. {ECO:0000269|PubMed:24814349, ECO:0000269|PubMed:25720052}.; ",{"$nulls":4},"p.Gln1484His","c.4452G>C","MODERATE","1484/1582",37,{"$nulls":5},"5","1028","718","787","563","897","621","0","0","0","0.5089",{"$nulls":20},"2.538955",".;.;-3.34;-3.34;.;.;.;.",".;.;1.02;.;.;.;.;.","0.999866",".;.;-1.71;-1.71;.;.;.;.",".;.;0.404;.;.;.;.;.",".;.;0.002;0.002;.;.;.;.",".;.;0.502;0.508;.;.;.;.",{"$nulls":3},"Unknown",-1,"AD/AR","Diabetes mellitus, transient neonatal, 2; Diabetes, permanent neonatal; Hyperinsulinemic hypoglycemia, familial, 1; Hypoglycemia, leucine-induced","Endocrine",{"$nulls":3},"C0271714| CN280869| C1835887| C0011860| C2931832| C1833104","0/0","1008,0","0","1008","0/1","332,362","0.5216","694",null,"chr11:17394362:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5151"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABCD4","chr14:74302911","ABCD4(start_lost)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: May be involved in intracellular processing of vitamin B12 (cobalamin). Could play a role in the lysosomal release of vitamin B12 into the cytoplasm. {ECO:0000269|PubMed:22922874}.; ",{"$nulls":4},"p.Met1?","c.2T>G","HIGH","1/606",1,{"$nulls":5},"4","579","373","372","240","514","325","0.0017","0.0017","0","0.0585",{"$nulls":5},"(ABCD4|ENSG00000119688|1|1.00)",{"$nulls":14},"3.4892440000000002","-3.32;-5.37",null,"1","0.19;-0.15","0.244;.","0.0","0.877;0.838",{"$nulls":3},"Unknown",-1,"AR","Methylmalonic aciduria and homocystinuria, cblJ type","Allergy/Immunology/Infectious; Biochemical; Cardiovascular; Neurologic",{"$nulls":3},"CN043592| C3553915","0/0","562,0","0","562","0/1","327,21","0.0603","348",null,"chr14:74302911:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0583"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABHD14B","chr3:51971467","ABHD14B(D68E)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Has hydrolase activity towards p-nitrophenyl butyrate (in vitro). May activate transcription. {ECO:0000269|PubMed:14672934}.; ",{"$nulls":5},"c.204C>A","HIGH",null,2,{"$nulls":5},"3",null,null,"149","83",{"$nulls":26},"3.312588","1.65;1.65;1.65;1.65;-1.1;1.65","3.51;.;3.51;3.51;.;3.51","0.999997","-3.86","0.999;.;0.999;0.999;0.999;0.999","0.0;0.0;0.0;0.0;0.002;0.0","0.992;0.979;0.986;0.992;0.993;0.986",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","151,0","0","151","0/1","80,5","0.0588","85",null,"chr3:51971467:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0602"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABHD16B","chr20:63862676","ABHD16B(Q379R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln379Arg","c.1136A>G","MODERATE","379/469",1,{"$nulls":5},"4","349","440",null,null,"162","249","0","0","0","0.1084",{"$nulls":20},"2.626837","0.86","1.4","0.721781","-1.26","0.605","0.312","0.194",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","358,0","0","358","0/1","408,30","0.0685","438",null,"chr20:63862676:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABHD16B","chr20:63862676","ABHD16B(Q379R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln379Arg","c.1136A>G","MODERATE","379/469",1,{"$nulls":5},"4","349","301",null,null,"163","201","0","0","0","0.2687",{"$nulls":20},"2.626837","0.86","1.4","0.721781","-1.26","0.605","0.312","0.194",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","355,0","0","355","0/1","242,60","0.1987","302",null,"chr20:63862676:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABI3BP","chr3:100770760","ABI3BP(L1566Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu1566Gln","c.4697T>A","MODERATE","1566/1777",61,{"$nulls":5},"5","550","866","420","656","474","747","0","0","0","0.162",{"$nulls":20},"1.794983","0.38",".;-0.05","0.999971;0.999952;0.999971","-1.24;-0.94","0.127;0.022","0.379;0.61","0.361;0.216",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","543,0","0","543","0/1","699,138","0.1649","837",null,"chr3:100770760:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1616"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABI3BP","chr3:100770760","ABI3BP(L1566Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu1566Gln","c.4697T>A","MODERATE","1566/1777",61,{"$nulls":5},"5","550","401","420","302","475","350","0","0","0","0.5343",{"$nulls":20},"1.794983","0.38",".;-0.05","0.999971;0.999952;0.999971","-1.24;-0.94","0.127;0.022","0.379;0.61","0.361;0.216",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","543,0","0","543","0/1","186,205","0.5243","391",null,"chr3:100770760:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ABLIM2","chr4:7967055","ABLIM2(E626Q)",{"$nulls":6},255,"PASS","Missense","rs761747422",5.189413596263622E-4,null,"FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity. {ECO:0000269|PubMed:17194709}.; ",{"$nulls":4},"p.Glu626Gln","c.1876G>C","MODERATE","626/646",21,{"$nulls":5},"5","370","301","248","203","333","261","0","0","0","0.2912",{"$nulls":20},"1.880001","1.53;0.86;1.71;1.78;1.74;1.47;.;1.51",".;.;.;1.99;.;.;.;.","0.808888;0.960448;0.956314;0.995507;0.977187;0.977187;0.977187;0.960448;0.99887;0.997227;0.764214","-0.96;-1.25;-1.07;-1.07;-1.0;-0.91;.;-0.9","0.996;0.785;.;0.403;0.993;.;.;.","0.803;0.745;0.9;0.83;0.746;0.789;.;1.0","0.223;0.161;0.225;0.193;0.195;0.167;0.335;0.32",{"$nulls":3},"ALSPAC_AF",5.189413596263622E-4,{"$nulls":7},"0/0","359,0","0","359","0/1","198,95","0.3242","293",null,"chr4:7967055:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3153"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ABLIM2","chr4:7967055","ABLIM2(E626Q)",{"$nulls":6},255,"PASS","Missense","rs761747422",5.189413596263622E-4,null,"FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity. {ECO:0000269|PubMed:17194709}.; ",{"$nulls":4},"p.Glu626Gln","c.1876G>C","MODERATE","626/646",21,{"$nulls":5},"5","370","165","248","117","337","136","0","0","0","0.6324",{"$nulls":20},"1.880001","1.53;0.86;1.71;1.78;1.74;1.47;.;1.51",".;.;.;1.99;.;.;.;.","0.808888;0.960448;0.956314;0.995507;0.977187;0.977187;0.977187;0.960448;0.99887;0.997227;0.764214","-0.96;-1.25;-1.07;-1.07;-1.0;-0.91;.;-0.9","0.996;0.785;.;0.403;0.993;.;.;.","0.803;0.745;0.9;0.83;0.746;0.789;.;1.0","0.223;0.161;0.225;0.193;0.195;0.167;0.335;0.32",{"$nulls":3},"ALSPAC_AF",5.189413596263622E-4,{"$nulls":7},"0/0","367,0","0","367","0/1","55,109","0.6646","164",null,"chr4:7967055:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6325"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ACE2","chrX:15573396","ACE2(F504L)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin- 13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. {ECO:0000269|PubMed:10924499, ECO:0000269|PubMed:10969042, ECO:0000269|PubMed:14647384, ECO:0000269|PubMed:24227843}.; FUNCTION: (Microbial infection) Acts as a receptor for Human coronavirus NL63/HCoV-NL63. {ECO:0000269|PubMed:15897467}.; ",{"$nulls":5},"c.1512C>G","HIGH",null,11,{"$nulls":5},"5","325","453","237","311","278","399","0","0","0","0.1454",{"$nulls":20},"3.317289","0.98","3.625","0.991777","-5.48","0.996","0.002","0.669",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","321,0","0","321","0/1","382,60","0.1357","442",null,"chrX:15573396:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1318"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ACE2","chrX:15573396","ACE2(F504L)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin- 13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. {ECO:0000269|PubMed:10924499, ECO:0000269|PubMed:10969042, ECO:0000269|PubMed:14647384, ECO:0000269|PubMed:24227843}.; FUNCTION: (Microbial infection) Acts as a receptor for Human coronavirus NL63/HCoV-NL63. {ECO:0000269|PubMed:15897467}.; ",{"$nulls":5},"c.1512C>G","HIGH",null,11,{"$nulls":5},"5","325","334","237","239","276","295","0","0","0","0.3119",{"$nulls":20},"3.317289","0.98","3.625","0.991777","-5.48","0.996","0.002","0.669",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","316,0","0","316","0/1","210,100","0.3226","310",null,"chrX:15573396:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.318"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ACTR5","chr20:38752272","ACTR5(S250fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Involved in DNA double-strand break repair and UV-damage excision repair. {ECO:0000269|PubMed:19014934, ECO:0000269|PubMed:20855601}.; ",{"$nulls":4},"p.Ser250fs","c.750_775delCTACATCGCTGAGGATTATGTGGAAG","HIGH","250/607",3,{"$nulls":5},"5","307","395","228","281","200","309","0","0","0","0.2201",{"$nulls":5},"(ACTR5|ENSG00000101442|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","335,0","0","335","0/1","332,70","0.1741","402",null,"chr20:38752272:CAGCTACATCGCTGAGGATTATGTGGA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1957"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ACTR5","chr20:38752272","ACTR5(S250fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Involved in DNA double-strand break repair and UV-damage excision repair. {ECO:0000269|PubMed:19014934, ECO:0000269|PubMed:20855601}.; ",{"$nulls":4},"p.Ser250fs","c.750_775delCTACATCGCTGAGGATTATGTGGAAG","HIGH","250/607",3,{"$nulls":5},"5","307","259","228","176","200","189","0","0","0","0.3228",{"$nulls":5},"(ACTR5|ENSG00000101442|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","335,0","0","335","0/1","179,79","0.3062","258",null,"chr20:38752272:CAGCTACATCGCTGAGGATTATGTGGA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3295"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ADAMTS20","chr12:43551262","ADAMTS20(V34L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in tissue-remodeling process occurring in both normal and pathological conditions. May have a protease- independent function in the transport from the endoplasmic reticulum to the Golgi apparatus of secretory cargos, mediated by the GON domain.; ",{"$nulls":4},"p.Val34Leu","c.100G>T","MODERATE","34/1910",2,{"$nulls":5},"5","253","347","197","268","239","321","0","0","0","0.0561",{"$nulls":20},"2.100946","0.42;0.25;.","1.845;.;.","0.983904","-0.49;-0.71;.",null,"0.709;0.645;.","0.296;0.274;0.256",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","249,0","0","249","0/1","303,24","0.0734","327",null,"chr12:43551262:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0709"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AFP","chr4:73452561","AFP(K530M)",null,null,"domain (Albumin 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Alpha-fetoprotein deficiency (AFPD) [MIM:615969]: A benign condition characterized by undetectable AFP levels in the amniotic fluid. Affected individuals are asymptomatic and present normal development. {ECO:0000269|PubMed:15280901, ECO:0000269|PubMed:18854864}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Alpha-fetoprotein, hereditary persistence (HPAFP) [MIM:615970]: A benign autosomal dominant condition characterized by continued expression of alpha-fetoprotein in adult life. {ECO:0000269|PubMed:7684942}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds copper, nickel, and fatty acids as well as, and bilirubin less well than, serum albumin. Only a small percentage (less than 2%) of the human AFP shows estrogen-binding properties.; ",{"$nulls":4},"p.Lys530Met","c.1589A>T","MODERATE","530/622",12,{"$nulls":5},"5","499","475","346","318","467","433","0","0","0","0.0693",{"$nulls":20},"2.94061","0.32","1.94;.","0.879936","0.71;0.81","1.0;.","0.133;0.209","0.401;0.405",{"$nulls":3},"Unknown",-1,"AD/AR","AFP deficiency, congenital; Hereditary persistence of AFP","General",{"$nulls":3},"C1863081| C1863080","0/0","489,0","0","489","0/1","421,37","0.0808","458",null,"chr4:73452561:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0755"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AGTPBP1","chr9:85677498","AGTPBP1(S177C)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes gene-encoded polyglutamates from the carboxy-terminus of target proteins such as MYLK. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5. {ECO:0000250|UniProtKB:Q641K1}.; ",{"$nulls":4},"p.Ser177Cys","c.530C>G","MODERATE","177/1278",5,1,{"$nulls":4},"4","466","551","286","326","364","428","0","0","0","0.0678",{"$nulls":20},"2.072164","0.83;.;0.68;.","2.28;.;2.28;.","0.999658;0.999658;0.99969;0.99969;0.999658;0.99969;0.99969","-2.35;-1.39;-2.35;.","0.997;.;0.999;0.999","0.015;0.009;0.013;.","0.402;0.401;0.308;0.424",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748934","0/0","435,0","0","435","0/1","468,35","0.0696","503",null,"chr9:85677498:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0675"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AHNAK2","chr14:104944264","AHNAK2(L3729F)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs368299595",2.594706798131811E-4,{"$nulls":6},"p.Leu3729Phe","c.11187G>C","MODERATE","3729/5795",7,{"$nulls":5},"4","1010","1258","820","955","538","612","0","0","0","0.1928",{"$nulls":20},"-0.031651","5.05","-0.1","1","0.08","0.001","0.325","0.045",{"$nulls":3},"ALSPAC_AF",2.594706798131811E-4,{"$nulls":7},"0/0","978,0","0","978","0/1","923,259","0.2191","1182",null,"chr14:104944264:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2115"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","AHNAK2","chr14:104944264","AHNAK2(L3729F)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs368299595",2.594706798131811E-4,{"$nulls":6},"p.Leu3729Phe","c.11187G>C","MODERATE","3729/5795",7,{"$nulls":5},"4","1010","1062","820","808","502","521","0","0","0","0.4664",{"$nulls":20},"-0.031651","5.05","-0.1","1","0.08","0.001","0.325","0.045",{"$nulls":3},"ALSPAC_AF",2.594706798131811E-4,{"$nulls":7},"0/0","985,0","0","985","0/1","572,444","0.437","1016",null,"chr14:104944264:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4121"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AIM1","chr6:106561470","AIM1(W2036C)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Trp2036Cys","c.6108G>C","MODERATE","2036/2131",20,{"$nulls":5},"5","255","363","171","237","225","336","0","0","0","0.2232",{"$nulls":20},"4.723322",".;0.99",null,"1",".;-12.16",".;1.0",".;0.0","0.918;0.935",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","252,0","0","252","0/1","263,85","0.2443","348",null,"chr6:106561470:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2278"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","AIM1","chr6:106561470","AIM1(W2036C)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Trp2036Cys","c.6108G>C","MODERATE","2036/2131",20,{"$nulls":5},"5","255","190","171","129","224","174","0","0","0","0.3506",{"$nulls":20},"4.723322",".;0.99",null,"1",".;-12.16",".;1.0",".;0.0","0.918;0.935",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","252,0","0","252","0/1","119,68","0.3636","187",null,"chr6:106561470:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3566"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AKAP13","chr15:85543778","AKAP13(G162V)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Scaffold protein that plays an important role in assembling signaling complexes downstream of several types of G protein-coupled receptors. Activates RHOA in response to signaling via G protein-coupled receptors via its function as Rho guanine nucleotide exchange factor (PubMed:11546812, PubMed:15229649, PubMed:23090968, PubMed:25186459, PubMed:24993829). May also activate other Rho family members (PubMed:11546812). Part of a kinase signaling complex that links ADRA1A and ADRA1B adrenergic receptor signaling to the activation of downstream p38 MAP kinases, such as MAPK11 and MAPK14 (PubMed:17537920, PubMed:23716597, PubMed:21224381). Part of a signaling complex that links ADRA1B signaling to the activation of RHOA and IKBKB/IKKB, leading to increased NF-kappa-B transcriptional activity (PubMed:23090968). Part of a RHOA-dependent signaling cascade that mediates responses to lysophosphatidic acid (LPA), a signaling molecule that activates G-protein coupled receptors and potentiates transcriptional activation of the glucocorticoid receptor NR3C1 (PubMed:16469733). Part of a signaling cascade that stimulates MEF2C-dependent gene expression in response to lysophosphatidic acid (LPA) (By similarity). Part of a signaling pathway that activates MAPK11 and/or MAPK14 and leads to increased transcription activation of the estrogen receptors ESR1 and ESR2 (PubMed:9627117, PubMed:11579095). Part of a signaling cascade that links cAMP and EGFR signaling to BRAF signaling and to PKA- mediated phosphorylation of KSR1, leading to the activation of downstream MAP kinases, such as MAPK1 or MAPK3 (PubMed:21102438). Functions as scaffold protein that anchors cAMP-dependent protein kinase (PKA) and PRKD1. This promotes activation of PRKD1, leading to increased phosphorylation of HDAC5 and ultimately cardiomyocyte hypertrophy (By similarity). Has no guanine nucleotide exchange activity on CDC42, Ras or Rac (PubMed:11546812). Required for normal embryonic heart development, and in particular for normal sarcomere formation in the developing cardiomyocytes (By similarity). Plays a role in cardiomyocyte growth and cardiac hypertrophy in response to activation of the beta-adrenergic receptor by phenylephrine or isoproterenol (PubMed:17537920, PubMed:23090968). Required for normal adaptive cardiac hypertrophy in response to pressure overload (PubMed:23716597). Plays a role in osteogenesis (By similarity). {ECO:0000250|UniProtKB:E9Q394, ECO:0000269|PubMed:11546812, ECO:0000269|PubMed:11579095, ECO:0000269|PubMed:17537920, ECO:0000269|PubMed:21224381, ECO:0000269|PubMed:23716597, ECO:0000269|PubMed:24993829, ECO:0000269|PubMed:25186459, ECO:0000269|PubMed:9627117, ECO:0000269|PubMed:9891067}.; ",{"$nulls":4},"p.Gly162Val","c.485G>T","MODERATE","162/2817",5,{"$nulls":5},"4","597","783","473","590","487","655","0","0","0","0.1038",{"$nulls":20},"1.508823","0.2",".;1.245;1.245","0.993267","-1.74;-2.51;-2.51",".;0.012;0.021","0.154;0.168;0.199",".;0.431;0.433",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","582,0","0","582","0/1","657,70","0.0963","727",null,"chr15:85543778:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","AKAP13","chr15:85543778","AKAP13(G162V)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Scaffold protein that plays an important role in assembling signaling complexes downstream of several types of G protein-coupled receptors. Activates RHOA in response to signaling via G protein-coupled receptors via its function as Rho guanine nucleotide exchange factor (PubMed:11546812, PubMed:15229649, PubMed:23090968, PubMed:25186459, PubMed:24993829). May also activate other Rho family members (PubMed:11546812). Part of a kinase signaling complex that links ADRA1A and ADRA1B adrenergic receptor signaling to the activation of downstream p38 MAP kinases, such as MAPK11 and MAPK14 (PubMed:17537920, PubMed:23716597, PubMed:21224381). Part of a signaling complex that links ADRA1B signaling to the activation of RHOA and IKBKB/IKKB, leading to increased NF-kappa-B transcriptional activity (PubMed:23090968). Part of a RHOA-dependent signaling cascade that mediates responses to lysophosphatidic acid (LPA), a signaling molecule that activates G-protein coupled receptors and potentiates transcriptional activation of the glucocorticoid receptor NR3C1 (PubMed:16469733). Part of a signaling cascade that stimulates MEF2C-dependent gene expression in response to lysophosphatidic acid (LPA) (By similarity). Part of a signaling pathway that activates MAPK11 and/or MAPK14 and leads to increased transcription activation of the estrogen receptors ESR1 and ESR2 (PubMed:9627117, PubMed:11579095). Part of a signaling cascade that links cAMP and EGFR signaling to BRAF signaling and to PKA- mediated phosphorylation of KSR1, leading to the activation of downstream MAP kinases, such as MAPK1 or MAPK3 (PubMed:21102438). Functions as scaffold protein that anchors cAMP-dependent protein kinase (PKA) and PRKD1. This promotes activation of PRKD1, leading to increased phosphorylation of HDAC5 and ultimately cardiomyocyte hypertrophy (By similarity). Has no guanine nucleotide exchange activity on CDC42, Ras or Rac (PubMed:11546812). Required for normal embryonic heart development, and in particular for normal sarcomere formation in the developing cardiomyocytes (By similarity). Plays a role in cardiomyocyte growth and cardiac hypertrophy in response to activation of the beta-adrenergic receptor by phenylephrine or isoproterenol (PubMed:17537920, PubMed:23090968). Required for normal adaptive cardiac hypertrophy in response to pressure overload (PubMed:23716597). Plays a role in osteogenesis (By similarity). {ECO:0000250|UniProtKB:E9Q394, ECO:0000269|PubMed:11546812, ECO:0000269|PubMed:11579095, ECO:0000269|PubMed:17537920, ECO:0000269|PubMed:21224381, ECO:0000269|PubMed:23716597, ECO:0000269|PubMed:24993829, ECO:0000269|PubMed:25186459, ECO:0000269|PubMed:9627117, ECO:0000269|PubMed:9891067}.; ",{"$nulls":4},"p.Gly162Val","c.485G>T","MODERATE","162/2817",5,{"$nulls":5},"4","597","535","473","421","487","445","0","0","0","0.2045",{"$nulls":20},"1.508823","0.2",".;1.245;1.245","0.993267","-1.74;-2.51;-2.51",".;0.012;0.021","0.154;0.168;0.199",".;0.431;0.433",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","582,0","0","582","0/1","411,105","0.2035","516",null,"chr15:85543778:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1971"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","AKAP17A","chrX:1594182","AKAP17A(M240I)",null,null,"domain (RRM )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Splice factor regulating alternative splice site selection for certain mRNA precursors. Mediates regulation of pre- mRNA splicing in a PKA-dependent manner. {ECO:0000269|PubMed:16982639, ECO:0000269|PubMed:19840947}.; ",{"$nulls":4},"p.Met240Ile","c.720G>A","MODERATE","240/695",2,{"$nulls":5},"5","543","567","413","429","488","533","0","0","0","0.2514",{"$nulls":20},"2.468476","0.83","2.485;.","1","-1.14;-1.0","0.552;.","0.02;0.042","0.747;0.695",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","539,0","0","539","0/1","408,151","0.2701","559",null,"chrX:1594182:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2681"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","AKAP17A","chrX:1594182","AKAP17A(M240I)",null,null,"domain (RRM )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Splice factor regulating alternative splice site selection for certain mRNA precursors. Mediates regulation of pre- mRNA splicing in a PKA-dependent manner. {ECO:0000269|PubMed:16982639, ECO:0000269|PubMed:19840947}.; ",{"$nulls":4},"p.Met240Ile","c.720G>A","MODERATE","240/695",2,{"$nulls":5},"5","543","428","413","333","486","402","0","0","0","0.1692",{"$nulls":20},"2.468476","0.83","2.485;.","1","-1.14;-1.0","0.552;.","0.02;0.042","0.747;0.695",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","538,0","0","538","0/1","347,76","0.1797","423",null,"chrX:1594182:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1682"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ALG1L","chr3:125933583","ALG1L(G51V)",{"$nulls":6},255,"PASS","Missense","rs151281228",2.2737608003638019E-4,null,"FUNCTION: Putative glycosyltransferase. {ECO:0000250}.; ",{"$nulls":4},"p.Gly51Val","c.152G>T","MODERATE","51/207",2,{"$nulls":5},"4","808","612","622","457","671","514","0","0","0","0.2529",{"$nulls":20},"2.41308",".;-0.4",".;0","0.969151",".;-2.15",".;0.25",".;0.004","0.367;0.395",{"$nulls":3},"ESP6500_AA_AF",2.2737608003638019E-4,{"$nulls":7},"0/0","782,0","0","782","0/1","441,136","0.2357","577",null,"chr3:125933583:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2276"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ANKRD61","chr7:6032876","ANKRD61(K85fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Lys85fs","c.254_265del<DELETE_NUC>insA","HIGH","85/418",2,{"$nulls":20},"6033063",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr7:6032876:<DELETE_NUC>:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","LOWQC","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ARAP2","chr4:36177832","ARAP2(E618K)",null,null,"domain (PH 2 )",{"$nulls":3},255,"PASS","Missense","rs765116606",2.6968716289104636E-4,null,"FUNCTION: Phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating protein that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members. Is activated by phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) binding. Can be activated by phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding, albeit with lower efficiency (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu618Lys","c.1852G>A","MODERATE","618/1704",9,1,{"$nulls":4},"4","108","75","108","75",null,null,"0","0",{"$nulls":22},"3.792312","1.55","1.635","0.809488","-2.05","1.0","0.158","0.614",{"$nulls":3},"TWINSUK_AF",2.6968716289104636E-4,{"$nulls":7},"0/0","107,0","0","107","0/1","66,9","0.12","75",null,"chr4:36177832:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.12"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ARFGAP1","chr20:63287847","ARFGAP1(D407N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: GTPase-activating protein (GAP) for the ADP ribosylation factor 1 (ARF1). Involved in membrane trafficking and /or vesicle transport. Promotes hydrolysis of the ARF1-bound GTP and thus, is required for the dissociation of coat proteins from Golgi-derived membranes and vesicles, a prerequisite for vesicle's fusion with target compartment. Probably regulates ARF1-mediated transport via its interaction with the KDELR proteins and TMED2. Overexpression induces the redistribution of the entire Golgi complex to the endoplasmic reticulum, as when ARF1 is deactivated. Its activity is stimulated by phosphoinosides and inhibited by phosphatidylcholine (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp407Asn","c.1219G>A","MODERATE","407/414",14,{"$nulls":5},"4","585","498","438","376","455","395","0","0","0","0.2101",{"$nulls":20},"2.92313","0.83;0.77;1.39;0.82;1.43",".;.;0.695;.;.","0.999069;0.999069;0.999069;0.999069;0.999069;1","-1.0;-1.27;-1.0;-1.13;-1.1",".;.;0.77;.;0.852","0.073;0.069;0.084;0.077;0.084","0.149;0.143;0.16;0.279;0.169",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","540,0","0","540","0/1","367,89","0.1952","456",null,"chr20:63287847:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1755"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ARSA","chr22:50626222","ARSA(K304M)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Metachromatic leukodystrophy (MLD) [MIM:250100]: An autosomal recessive disease caused by abnormal intralysosomal accumulation of cerebroside-3-sulfate in central and peripheral nervous systems, as well as other organs. MLD is clinically characterized by leukodystrophy, progressive demyelination and a variety of neurological symptoms, including gait disturbances, ataxias, optical atrophy, dementia, seizures, and spastic tetraparesis. Decreased arylsulfatase A activity is detected in urine, leukocytes, and fibroblasts of affected individuals. Several forms of the disease can be distinguished according to the age at onset and disease severity: late infantile, juvenile and adult forms, partial cerebroside sulfate deficiency, and pseudoarylsulfatase A deficiency. Individuals with pseudoarylsulfatase A deficiency have low arylsulfatase A activity but lack neurological manifestations and are apparently healthy. {ECO:0000269|PubMed:10220151, ECO:0000269|PubMed:10381328, ECO:0000269|PubMed:10477432, ECO:0000269|PubMed:10533072, ECO:0000269|PubMed:10751093, ECO:0000269|PubMed:11020646, ECO:0000269|PubMed:11061266, ECO:0000269|PubMed:11456299, ECO:0000269|PubMed:11941485, ECO:0000269|PubMed:12503099, ECO:0000269|PubMed:12788103, ECO:0000269|PubMed:1353340, ECO:0000269|PubMed:14517960, ECO:0000269|PubMed:14680985, ECO:0000269|PubMed:15026521, ECO:0000269|PubMed:15326627, ECO:0000269|PubMed:15710861, ECO:0000269|PubMed:1670590, ECO:0000269|PubMed:1673291, ECO:0000269|PubMed:1678251, ECO:0000269|PubMed:18693274, ECO:0000269|PubMed:19606494, ECO:0000269|PubMed:20339381, ECO:0000269|PubMed:21265945, ECO:0000269|PubMed:2574462, ECO:0000269|PubMed:7581401, ECO:0000269|PubMed:7825603, ECO:0000269|PubMed:7860068, ECO:0000269|PubMed:7902317, ECO:0000269|PubMed:7906588, ECO:0000269|PubMed:7909527, ECO:0000269|PubMed:8095918, ECO:0000269|PubMed:8101038, ECO:0000269|PubMed:8101083, ECO:0000269|PubMed:8104633, ECO:0000269|PubMed:8891236, ECO:0000269|PubMed:9090526, ECO:0000269|PubMed:9272717, ECO:0000269|PubMed:9452102, ECO:0000269|PubMed:9490297, ECO:0000269|PubMed:9600244, ECO:0000269|PubMed:9819708}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple sulfatase deficiency (MSD) [MIM:272200]: A clinically and biochemically heterogeneous disorder caused by the simultaneous impairment of all sulfatases, due to defective post- translational modification and activation. It combines features of individual sulfatase deficiencies such as metachromatic leukodystrophy, mucopolysaccharidosis, chondrodysplasia punctata, hydrocephalus, ichthyosis, neurologic deterioration and developmental delay. {ECO:0000269|PubMed:15146462}. Note=The protein represented in this entry is involved in disease pathogenesis. Arylsulfatase A activity is impaired in multiple sulfatase deficiency due to mutations in SUMF1 (PubMed:15146462). SUMF1 mutations result in defective post-translational modification of ARSA at residue Cys-69 that is not converted to 3- oxoalanine (PubMed:7628016). {ECO:0000269|PubMed:15146462, ECO:0000269|PubMed:7628016}.; ","FUNCTION: Hydrolyzes cerebroside sulfate. {ECO:0000269|PubMed:10751093}.; ",{"$nulls":4},"p.Lys304Met","c.911A>T","MODERATE","304/509",5,{"$nulls":5},"5","525","308","378","223","488","268","0","0","0","0.4328",{"$nulls":20},"3.811823","-4.42",null,"1","-5.86",null,"0.0","0.844;0.844;0.844;0.86;0.844",{"$nulls":3},"Unknown",-1,"AR","Metachromatic leukodystrophy","Biochemical; Neurologic",{"$nulls":3},"C0023522","0/0","517,0","0","517","0/1","172,129","0.4286","301",null,"chr22:50626222:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.417"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ATAD2","chr8:123328228","ATAD2(S1277F)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.; ",{"$nulls":4},"p.Ser1277Phe","c.3830C>T","MODERATE","1277/1390",25,{"$nulls":5},"5","85","114","79","97","70","82","0","0","0","0.122",{"$nulls":20},"2.051818","-3.0;1.42","2.19;.","0.999782","-1.85;-2.19","0.009;.","0.034;0.082","0.146;0.13",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","86,0","0","86","0/1","96,13","0.1193","109",null,"chr8:123328228:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1134"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ATAD2","chr8:123328228","ATAD2(S1277F)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.; ",{"$nulls":4},"p.Ser1277Phe","c.3830C>T","MODERATE","1277/1390",25,{"$nulls":5},"4","85","67","79","61",null,null,"0","0",{"$nulls":22},"2.051818","-3.0;1.42","2.19;.","0.999782","-1.85;-2.19","0.009;.","0.034;0.082","0.146;0.13",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","86,0","0","86","0/1","54,13","0.194","67",null,"chr8:123328228:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1967"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ATF7IP","chr12:14424420","ATF7IP(A177P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. Can both act as an activator or a repressor depending on the context. Mediates MBD1-dependent transcriptional repression, probably by recruiting complexes containing SETDB1. Required to stimulate histone methyltransferase activity of SETDB1 and facilitate the conversion of dimethylated to trimethylated H3 'Lys-9' (H3K9me3). The complex formed with MBD1 and SETDB1 represses transcription and couples DNA methylation and histone H3 'Lys-9' trimethylation (H3K9me3). Facilitates telomerase TERT and TERC gene expression by SP1 in cancer cells. {ECO:0000269|PubMed:12665582, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:19106100}.; ",{"$nulls":4},"p.Ala177Pro","c.529G>C","MODERATE","177/1278",2,{"$nulls":5},"4","576","1425","446","1066","373","932","0","0","0","0.0933",{"$nulls":20},"0.114529","2.31;2.32;2.33;.;2.31;.;.;1.97;2.31","-0.895;-0.895;-0.895;.;.;.;.;.;-0.895","1","0.3;0.06;0.26;1.71;0.3;1.89;1.56;0.9;0.3","0.0;0.0;.;.;.;.;.;.;0.0","0.257;0.262;0.257;0.266;0.257;0.041;0.266;0.26;0.257","0.036;0.031;0.05;.;0.046;.;.;.;0.037",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","558,0","0","558","0/1","1262,102","0.0748","1364",null,"chr12:14424420:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.076"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ATP4A","chr19:35560588","ATP4A(K188*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1195049939",-1,null,"FUNCTION: Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.; ",{"$nulls":4},"p.Lys188*","c.562A>T","HIGH","188/1035",6,{"$nulls":5},"4","368","421","270","308","358","401","0","0","0","0.0599",{"$nulls":5},"(ATP4A|ENSG00000105675|1|1.00)","(ATP4A|ENSG00000105675|1|1.00)",{"$nulls":13},"7.215394",null,null,"1",{"$nulls":3},"0.91",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","353,0","0","353","0/1","371,30","0.0748","401",null,"chr19:35560588:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0649"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","AWAT2","chrX:70043525","AWAT2(G142E)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Acyltransferase that predominantly esterify long chain (wax) alcohols with acyl-CoA-derived fatty acids to produce wax esters. Wax esters are enriched in sebum, suggesting that it plays a central role in lipid metabolism in skin. Has no activity using decyl alcohol and significantly prefers the C16 and C18 alcohols. May also have 2-acylglycerol O-acyltransferase (MGAT) and acyl- CoA:retinol acyltransferase (ARAT) activities, to catalyze the synthesis of diacylglycerols and retinyl esters; however this activity is unclear in vivo. {ECO:0000269|PubMed:15220349, ECO:0000269|PubMed:15671038, ECO:0000269|PubMed:16106050}.; ",{"$nulls":4},"p.Gly142Glu","c.425G>A","MODERATE","142/333",4,{"$nulls":5},"3","555","287",{"$nulls":4},"0.0018","0.0018",{"$nulls":22},"1.321106","2.62","1.125","0.947668","-0.2","0.793","0.358","0.446",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","538,1","0.0019","539","0/1","178,91","0.3383","269",null,"chrX:70043525:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","B4GALNT3","chr12:545440","B4GALNT3(G204R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transfers N-acetylgalactosamine (GalNAc) from UDP-GalNAc to N-acetylglucosamine-beta-benzyl with a beta-1,4-linkage to form N,N'-diacetyllactosediamine, GalNAc-beta-1,4-GlcNAc structures in N-linked glycans and probably O-linked glycans. Mediates the N,N'- diacetyllactosediamine formation on gastric mucosa. {ECO:0000269|PubMed:16728562}.; ",{"$nulls":4},"p.Gly204Arg","c.610G>C","MODERATE","204/998",6,{"$nulls":5},"5","466","359","318","246","409","305","0","0","0","0.1639",{"$nulls":20},"4.043228","1.19","1.89;.","0.970966","-3.27;-3.73","0.991;0.994","0.02;0.043","0.671;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","457,0","0","457","0/1","280,66","0.1908","346",null,"chr12:545440:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1789"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","BDKRB1","chr14:96264698","BDKRB1(S339C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: This is a receptor for bradykinin. Could be a factor in chronic pain and inflammation.; ",{"$nulls":4},"p.Ser339Cys","c.1016C>G","MODERATE","339/353",3,{"$nulls":5},"5","466","546","332","374","418","471","0","0","0","0.2675",{"$nulls":20},"1.805069","1.01;.","0.805","1","-2.04;.","0.951","0.056;.","0.12;0.118",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Bradykinin, a 9 aa peptide, is generated in pathophysiologic conditions such as inflammation, trauma, burns, shock, and allergy. Two types of G-protein coupled receptors have been found which bind bradykinin and mediate responses to these pathophysiologic conditions. The protein encoded by this gene is one of these receptors and is synthesized de novo following tissue injury. Receptor binding leads to an increase in the cytosolic calcium ion concentration, ultimately resulting in chronic and acute inflammatory responses. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011].  ",null,null,"0/0","455,0","0","455","0/1","376,148","0.2824","524",null,"chr14:96264698:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2834"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","BDKRB1","chr14:96264698","BDKRB1(S339C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: This is a receptor for bradykinin. Could be a factor in chronic pain and inflammation.; ",{"$nulls":4},"p.Ser339Cys","c.1016C>G","MODERATE","339/353",3,{"$nulls":5},"5","466","253","332","176","407","223","0","0","0","0.6413",{"$nulls":20},"1.805069","1.01;.","0.805","1","-2.04;.","0.951","0.056;.","0.12;0.118",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Bradykinin, a 9 aa peptide, is generated in pathophysiologic conditions such as inflammation, trauma, burns, shock, and allergy. Two types of G-protein coupled receptors have been found which bind bradykinin and mediate responses to these pathophysiologic conditions. The protein encoded by this gene is one of these receptors and is synthesized de novo following tissue injury. Receptor binding leads to an increase in the cytosolic calcium ion concentration, ultimately resulting in chronic and acute inflammatory responses. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011].  ",null,null,"0/0","455,0","0","455","0/1","89,157","0.6382","246",null,"chr14:96264698:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.642"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","BEST2","chr19:12752673","BEST2(S27R)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Forms calcium-sensitive chloride channels. Permeable to bicarbonate. {ECO:0000269|PubMed:11904445, ECO:0000269|PubMed:12907679, ECO:0000269|PubMed:18400985}.; ",{"$nulls":4},"p.Ser27Arg","c.81C>G","MODERATE","27/509",1,{"$nulls":5},"5","721","689","488","475","666","615","0","0","0","0.1252",{"$nulls":20},"3.808684","-5.44","3.875","0.999999","-4.58","1.0","0.0","0.932;0.932;0.949",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","703,0","0","703","0/1","566,83","0.1279","649",null,"chr19:12752673:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1326"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","BIRC6","chr2:32467555","BIRC6(G1796V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase. Has an unusual ubiquitin conjugation system in that it could combine in a single polypeptide, ubiquitin conjugating (E2) with ubiquitin ligase (E3) activity, forming a chimeric E2/E3 ubiquitin ligase. Its tragets include CASP9 and DIABLO/SMAC. Acts as an inhibitor of CASP3, CASP7 and CASP9. Important regulator for the final stages of cytokinesis. Crucial for normal vesicle targeting to the site of abscission, but also for the integrity of the midbody and the midbody ring, and its striking ubiquitin modification. {ECO:0000269|PubMed:14765125, ECO:0000269|PubMed:15200957, ECO:0000269|PubMed:18329369}.; ",{"$nulls":4},"p.Gly1796Val","c.5387G>T","MODERATE","1796/4857",27,{"$nulls":5},"5","413","529","344","440","330","442","0","0","0","0.0611",{"$nulls":20},"3.969727","-1.68",null,"1","-7.63",null,null,"0.939",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","404,1","0.0025","405","0/1","489,31","0.0596","520",null,"chr2:32467555:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0523"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C11orf24","chr11:68262507","C11orf24(T163K)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr163Lys","c.488C>A","MODERATE","163/449",4,{"$nulls":5},"5","294","328","245","254","197","219","0","0","0","0.242",{"$nulls":20},"0.50634","1.21",null,"1","-0.53","0.018","0.031","0.042",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","290,0","0","290","0/1","238,87","0.2677","325",null,"chr11:68262507:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2677"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C11orf24","chr11:68262507","C11orf24(T163K)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr163Lys","c.488C>A","MODERATE","163/449",4,{"$nulls":5},"5","294","261","245","198","197","159","0","0","0","0.283",{"$nulls":20},"0.50634","1.21",null,"1","-0.53","0.018","0.031","0.042",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","290,0","0","290","0/1","166,96","0.3664","262",null,"chr11:68262507:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3535"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C15orf48","chr15:45432109","C15orf48(V54M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Val54Met","c.160G>A","MODERATE","54/131",4,{"$nulls":5},"5","183","206","123","129","168","188","0","0","0","0.2181",{"$nulls":20},"2.781358","-1.13",null,"0.951187","-1.08;-1.38;-1.08",null,"0.005;0.086;0.005","0.592;.;0.592",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","178,0","0","178","0/1","150,44","0.2268","194",null,"chr15:45432109:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2171"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C15orf48","chr15:45432109","C15orf48(V54M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Val54Met","c.160G>A","MODERATE","54/131",4,{"$nulls":5},"5","183","106","123","76","168","103","0","0","0","0.4175",{"$nulls":20},"2.781358","-1.13",null,"0.951187","-1.08;-1.38;-1.08",null,"0.005;0.086;0.005","0.592;.;0.592",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","178,0","0","178","0/1","58,44","0.4314","102",null,"chr15:45432109:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4079"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C1orf159","chr1:1085944","C1orf159(V163I)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense","rs1451207840",-1,{"$nulls":6},"p.Val163Ile","c.487G>A","MODERATE","163/380",9,1,{"$nulls":4},"5","441","440","329","297","393","380","0","0","0","0.0895",{"$nulls":20},"2.918013",null,"2.365;.;.;.;.","0.9919;0.9919;0.996368;0.9919;0.9919;0.9919;0.996368","-0.91;-0.89;-0.91;-0.89;-0.89","0.975;0.972;0.975;0.972;0.868","0.0","0.372;0.37;0.447;0.395;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","430,0","0","430","0/1","379,39","0.0933","418",null,"chr1:1085944:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.101"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C1orf228","chr1:44689883","C1orf228(L62F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu62Phe","c.186G>C","MODERATE","62/440",3,1,{"$nulls":4},"5","319","296","212","188","299","279","0","0","0","0.1613",{"$nulls":20},"3.056586",null,null,"0.844467","-3.16;-2.75;-2.89;-2.75;-2.89;-3.41",".;0.992;.;0.992;.;.","0.008;0.007;0.008;0.007;0.008;0.008",".;0.458;.;0.458;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","310,0","0","310","0/1","243,41","0.1444","284",null,"chr1:44689883:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1809"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C1orf228","chr1:44689883","C1orf228(L62F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu62Phe","c.186G>C","MODERATE","62/440",3,1,{"$nulls":4},"5","319","140","212","85","298","121","0","0","0","0.6033",{"$nulls":20},"3.056586",null,null,"0.844467","-3.16;-2.75;-2.89;-2.75;-2.89;-3.41",".;0.992;.;0.992;.;.","0.008;0.007;0.008;0.007;0.008;0.008",".;0.458;.;0.458;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","313,0","0","313","0/1","55,81","0.5956","136",null,"chr1:44689883:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5882"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C1S","chr12:7062557","C1S(Q30E)",{"$nulls":6},255,"PASS","Missense","rs143729983",7.5642965204236008E-4,"DISEASE: Complement component C1s deficiency (C1SD) [MIM:613783]: A rare defect resulting in C1 deficiency and impaired activation of the complement classical pathway. C1 deficiency generally leads to severe immune complex disease with features of systemic lupus erythematosus and glomerulonephritis. {ECO:0000269|PubMed:11390518}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ehlers-Danlos syndrome, periodontal type, 2 (EDSPD2) [MIM:617174]: A form of Ehlers-Danlos syndrome, a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDSPD2 is characterized by the association of typical features of Ehlers-Danlos syndrome with gingival recession and severe early- onset periodontal disease, leading to premature loss of permanent teeth. EDSPD2 transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27745832}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: C1s B chain is a serine protease that combines with C1q and C1r to form C1, the first component of the classical pathway of the complement system. C1r activates C1s so that it can, in turn, activate C2 and C4.; ",{"$nulls":4},"p.Gln30Glu","c.88C>G","MODERATE","30/688",3,1,{"$nulls":4},"5","570","908","420","669","501","789","0","0","0","0.2269",{"$nulls":20},"2.056653","1.41;1.41;1.41;.;1.41;1.41;1.41","1.03;1.03;1.03;.;.;.;.","0.99823;0.99823;0.99823;1","-0.56;-0.56;-0.56;.;-0.93;-1.0;-0.27","0.027;0.027;0.027;.;.;.;.","0.598;0.598;0.598;.;0.386;0.977;0.774","0.484;0.484;0.529;0.431;.;.;.",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,"AR","Complement component C1s deficiency","Allergy/Immunology/Infectious; Renal",{"$nulls":3},"C4310681| C3151078","0/0","557,0","0","557","0/1","674,196","0.2253","870",null,"chr12:7062557:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2197"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C1S","chr12:7062557","C1S(Q30E)",{"$nulls":6},255,"PASS","Missense","rs143729983",7.5642965204236008E-4,"DISEASE: Complement component C1s deficiency (C1SD) [MIM:613783]: A rare defect resulting in C1 deficiency and impaired activation of the complement classical pathway. C1 deficiency generally leads to severe immune complex disease with features of systemic lupus erythematosus and glomerulonephritis. {ECO:0000269|PubMed:11390518}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ehlers-Danlos syndrome, periodontal type, 2 (EDSPD2) [MIM:617174]: A form of Ehlers-Danlos syndrome, a connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. EDSPD2 is characterized by the association of typical features of Ehlers-Danlos syndrome with gingival recession and severe early- onset periodontal disease, leading to premature loss of permanent teeth. EDSPD2 transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27745832}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: C1s B chain is a serine protease that combines with C1q and C1r to form C1, the first component of the classical pathway of the complement system. C1r activates C1s so that it can, in turn, activate C2 and C4.; ",{"$nulls":4},"p.Gln30Glu","c.88C>G","MODERATE","30/688",3,1,{"$nulls":4},"5","570","650","420","486","499","573","0","0","0","0.4852",{"$nulls":20},"2.056653","1.41;1.41;1.41;.;1.41;1.41;1.41","1.03;1.03;1.03;.;.;.;.","0.99823;0.99823;0.99823;1","-0.56;-0.56;-0.56;.;-0.93;-1.0;-0.27","0.027;0.027;0.027;.;.;.;.","0.598;0.598;0.598;.;0.386;0.977;0.774","0.484;0.484;0.529;0.431;.;.;.",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,"AR","Complement component C1s deficiency","Allergy/Immunology/Infectious; Renal",{"$nulls":3},"C4310681| C3151078","0/0","560,0","0","560","0/1","322,300","0.4823","622",null,"chr12:7062557:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4691"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C2orf83","chr2:227611504","C2orf83(L115V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu115Val","c.343C>G","MODERATE","115/150",3,{"$nulls":5},"5","664","779","503","557","585","682","0","0","0","0.2126",{"$nulls":20},"1.11014",null,null,"1",null,"0.436",{"$nulls":5},"Unknown",-1,{"$nulls":7},"0/0","644,0","0","644","0/1","583,159","0.2143","742",null,"chr2:227611504:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2029"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C2orf83","chr2:227611504","C2orf83(L115V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu115Val","c.343C>G","MODERATE","115/150",3,{"$nulls":5},"5","664","346","503","256","585","311","0","0","0","0.254",{"$nulls":20},"1.11014",null,null,"1",null,"0.436",{"$nulls":5},"Unknown",-1,{"$nulls":7},"0/0","644,0","0","644","0/1","237,89","0.273","326",null,"chr2:227611504:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2734"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C3","chr19:6678277","C3(E1575D)",null,null,"domain (NTR ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs773903830",8.642e-05,"DISEASE: Complement component 3 deficiency (C3D) [MIM:613779]: A rare defect of the complement classical pathway. Patients develop recurrent, severe, pyogenic infections because of ineffective opsonization of pathogens. Some patients may also develop autoimmune disorders, such as arthralgia and vasculitic rashes, lupus-like syndrome and membranoproliferative glomerulonephritis. {ECO:0000269|PubMed:7961791}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Macular degeneration, age-related, 9 (ARMD9) [MIM:611378]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269|PubMed:17634448, ECO:0000269|PubMed:24036952}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hemolytic uremic syndrome atypical 5 (AHUS5) [MIM:612925]: An atypical form of hemolytic uremic syndrome. It is a complex genetic disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, renal failure and absence of episodes of enterocolitis and diarrhea. In contrast to typical hemolytic uremic syndrome, atypical forms have a poorer prognosis, with higher death rates and frequent progression to end-stage renal disease. {ECO:0000269|PubMed:18796626, ECO:0000269|PubMed:20513133}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Other genes may play a role in modifying the phenotype.; DISEASE: Note=Increased levels of C3 and its cleavage product ASP, are associated with obesity, diabetes and coronary heart disease. Short-term endurance training reduces baseline ASP levels and subsequently fat storage.; ","FUNCTION: C3 plays a central role in the activation of the complement system. Its processing by C3 convertase is the central reaction in both classical and alternative complement pathways. After activation C3b can bind covalently, via its reactive thioester, to cell surface carbohydrates or immune aggregates.; FUNCTION: C3-beta-c: Acts as a chemoattractant for neutrophils in chronic inflammation. {ECO:0000250}.; ",{"$nulls":4},"p.Glu1575Asp","c.4725G>C","MODERATE","1575/1663",40,{"$nulls":5},"4","629","647","525","498","551","537","0","0","0","0.298",{"$nulls":20},"1.7202250000000001","1.96","1.71","0.886631","-0.42","0.002","0.582","0.304",{"$nulls":3},"ExAC_AMR_AF",8.642e-05,"AR","Complement component 3 deficiency, autosomal recessive; Hemolytic uremic syndrome, atypical, susceptibility to, 5","Allergy/Immunology/Infectious; Hematologic; Ophthalmologic;  Renal",null,"putative complement component C3; likely involved in innate immune response [RGD, Feb 2006].  ",null,"C1969651| C2752037| C3151071","0/0","624,0","0","624","0/1","422,202","0.3237","624",null,"chr19:6678277:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3213"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C3","chr19:6678277","C3(E1575D)",null,null,"domain (NTR ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs773903830",8.642e-05,"DISEASE: Complement component 3 deficiency (C3D) [MIM:613779]: A rare defect of the complement classical pathway. Patients develop recurrent, severe, pyogenic infections because of ineffective opsonization of pathogens. Some patients may also develop autoimmune disorders, such as arthralgia and vasculitic rashes, lupus-like syndrome and membranoproliferative glomerulonephritis. {ECO:0000269|PubMed:7961791}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Macular degeneration, age-related, 9 (ARMD9) [MIM:611378]: A form of age-related macular degeneration, a multifactorial eye disease and the most common cause of irreversible vision loss in the developed world. In most patients, the disease is manifest as ophthalmoscopically visible yellowish accumulations of protein and lipid that lie beneath the retinal pigment epithelium and within an elastin-containing structure known as Bruch membrane. {ECO:0000269|PubMed:17634448, ECO:0000269|PubMed:24036952}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hemolytic uremic syndrome atypical 5 (AHUS5) [MIM:612925]: An atypical form of hemolytic uremic syndrome. It is a complex genetic disease characterized by microangiopathic hemolytic anemia, thrombocytopenia, renal failure and absence of episodes of enterocolitis and diarrhea. In contrast to typical hemolytic uremic syndrome, atypical forms have a poorer prognosis, with higher death rates and frequent progression to end-stage renal disease. {ECO:0000269|PubMed:18796626, ECO:0000269|PubMed:20513133}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Other genes may play a role in modifying the phenotype.; DISEASE: Note=Increased levels of C3 and its cleavage product ASP, are associated with obesity, diabetes and coronary heart disease. Short-term endurance training reduces baseline ASP levels and subsequently fat storage.; ","FUNCTION: C3 plays a central role in the activation of the complement system. Its processing by C3 convertase is the central reaction in both classical and alternative complement pathways. After activation C3b can bind covalently, via its reactive thioester, to cell surface carbohydrates or immune aggregates.; FUNCTION: C3-beta-c: Acts as a chemoattractant for neutrophils in chronic inflammation. {ECO:0000250}.; ",{"$nulls":4},"p.Glu1575Asp","c.4725G>C","MODERATE","1575/1663",40,{"$nulls":5},"4","629","311","525","250","549","258","0","0","0","0.624",{"$nulls":20},"1.7202250000000001","1.96","1.71","0.886631","-0.42","0.002","0.582","0.304",{"$nulls":3},"ExAC_AMR_AF",8.642e-05,"AR","Complement component 3 deficiency, autosomal recessive; Hemolytic uremic syndrome, atypical, susceptibility to, 5","Allergy/Immunology/Infectious; Hematologic; Ophthalmologic;  Renal",null,"putative complement component C3; likely involved in innate immune response [RGD, Feb 2006].  ",null,"C1969651| C2752037| C3151071","0/0","623,0","0","623","0/1","121,189","0.6097","310",null,"chr19:6678277:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.624"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C8orf33","chr8:145052497","C8orf33(Sequence Feature)",{"$nulls":3},"modified-residue:N-acetylalanine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,{"$nulls":7},"c.6G>T","MODERATE",null,1,{"$nulls":5},"5","308","291","237","216","210","217","0","0","0","0.0645",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","300,0","0","300","0/1","270,17","0.0592","287",null,"chr8:145052497:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0602"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C8orf33","chr8:145052497","C8orf33(Sequence Feature)",{"$nulls":3},"modified-residue:N-acetylalanine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,{"$nulls":7},"c.6G>T","MODERATE",null,1,{"$nulls":5},"5","308","270","237","199","208","177","0","0","0","0.565",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","300,0","0","300","0/1","114,147","0.5632","261",null,"chr8:145052497:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5477"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","C8orf33","chr8:145053358","C8orf33(K155N)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys155Asn","c.465G>C","MODERATE","155/229",4,{"$nulls":5},"4","624","727","457","518","559","648","0","0","0","0.1435",{"$nulls":20},"2.967081",null,"3.255;.;.;.;.","0.999989","-4.63;.;.;.;.","1.0;.;.;.;.","0.0;.;.;.;.","0.451;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","619,0","0","619","0/1","609,99","0.1398","708",null,"chr8:145053358:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1293"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","C8orf33","chr8:145053358","C8orf33(K155N)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys155Asn","c.465G>C","MODERATE","155/229",4,{"$nulls":5},"4","624","515","457","386","556","464","0","0","0","0.1595",{"$nulls":20},"2.967081",null,"3.255;.;.;.;.","0.999989","-4.63;.;.;.;.","1.0;.;.;.;.","0.0;.;.;.;.","0.451;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","617,0","0","617","0/1","424,78","0.1554","502",null,"chr8:145053358:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1658"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CABIN1","chr22:24072473","CABIN1(C866fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May be required for replication-independent chromatin assembly. May serve as a negative regulator of T-cell receptor (TCR) signaling via inhibition of calcineurin. Inhibition of activated calcineurin is dependent on both PKC and calcium signals. Acts as a negative regulator of p53/TP53 by keeping p53 in an inactive state on chromatin at promoters of a subset of it's target genes. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:9655484}.; ",{"$nulls":4},"p.Cys866fs","c.2596_2602delTGCCACC","HIGH","866/2220",18,{"$nulls":5},"5","386","461","268","301","312","368","0.0026","0.0026","0","0.1196",{"$nulls":5},"(CABIN1|ENSG00000099991|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","393,0","0","393","0/1","370,54","0.1274","424",null,"chr22:24072473:GTGCCACC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1296"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CABIN1","chr22:24072473","CABIN1(C866fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May be required for replication-independent chromatin assembly. May serve as a negative regulator of T-cell receptor (TCR) signaling via inhibition of calcineurin. Inhibition of activated calcineurin is dependent on both PKC and calcium signals. Acts as a negative regulator of p53/TP53 by keeping p53 in an inactive state on chromatin at promoters of a subset of it's target genes. {ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:9655484}.; ",{"$nulls":4},"p.Cys866fs","c.2596_2602delTGCCACC","HIGH","866/2220",18,{"$nulls":5},"5","386","350","268","216","311","271","0.0026","0.0026","0","0.1882",{"$nulls":5},"(CABIN1|ENSG00000099991|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","393,0","0","393","0/1","267,61","0.186","328",null,"chr22:24072473:GTGCCACC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.162"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CACNA1I","chr22:39670080","CACNA1I(S1413A)",null,null,"transmembrane region (Helical; Name=S6 of repeat III ), repeat (III )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This channel gives rise to T-type calcium currents. T-type calcium channels belong to the \"low-voltage activated (LVA)\" group and are strongly blocked by nickel and mibefradil. A particularity of this type of channels is an opening at quite negative potentials, and a voltage- dependent inactivation. T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle. They may also be involved in the modulation of firing patterns of neurons which is important for information processing as well as in cell growth processes. Gates in voltage ranges similar to, but higher than alpha 1G or alpha 1H (By similarity). {ECO:0000250}.; ","level2",{"$nulls":3},"p.Ser1413Ala","c.4237T>G","MODERATE","1413/2223",25,{"$nulls":5},"4","703","683","524","489","590","563","0","0","0","0.3055",{"$nulls":20},"4.053632","-5.04",".;1.475;.;1.475","0.999992;0.999726;0.999992;0.999726;0.999992;0.999726","-2.96;-2.94;-2.94;-2.94","0.99;0.009;0.996;0.994","0.158;0.15;0.135;0.133","0.606;0.582;0.599;0.576",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","686,0","0","686","0/1","440,208","0.321","648",null,"chr22:39670080:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.319"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CACNA1I","chr22:39670080","CACNA1I(S1413A)",null,null,"transmembrane region (Helical; Name=S6 of repeat III ), repeat (III )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This channel gives rise to T-type calcium currents. T-type calcium channels belong to the \"low-voltage activated (LVA)\" group and are strongly blocked by nickel and mibefradil. A particularity of this type of channels is an opening at quite negative potentials, and a voltage- dependent inactivation. T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle. They may also be involved in the modulation of firing patterns of neurons which is important for information processing as well as in cell growth processes. Gates in voltage ranges similar to, but higher than alpha 1G or alpha 1H (By similarity). {ECO:0000250}.; ","level2",{"$nulls":3},"p.Ser1413Ala","c.4237T>G","MODERATE","1413/2223",25,{"$nulls":5},"4","703","341","524","255","587","273","0","0","0","0.6557",{"$nulls":20},"4.053632","-5.04",".;1.475;.;1.475","0.999992;0.999726;0.999992;0.999726;0.999992;0.999726","-2.96;-2.94;-2.94;-2.94","0.99;0.009;0.996;0.994","0.158;0.15;0.135;0.133","0.606;0.582;0.599;0.576",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","693,0","0","693","0/1","108,220","0.6707","328",null,"chr22:39670080:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6745"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CAMTA2","chr17:4980525","CAMTA2(H289L)",null,null,"compositionally biased region (Ser-rich ), splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription activator. May act as tumor suppressor. {ECO:0000269|PubMed:11925432}.; ",{"$nulls":4},"p.His289Leu","c.866A>T","MODERATE","289/1241",9,{"$nulls":5},"3","194","179",{"$nulls":4},"0","0",{"$nulls":22},"0.878444","0.84",".;.;.;.;0","0.998912;0.995652;0.995652;0.995652;0.995652;0.995652","-4.66;-4.75;.;-4.66;-4.76",".;0.978;.;0.763;0.651","0.023;0.042;.;0.049;0.046","0.349;0.353;0.31;0.302;0.352",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","174,0","0","174","0/1","122,20","0.1408","142",null,"chr17:4980525:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CAPS2","chr12:75291815","CAPS2(A409V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala409Val","c.1226C>T","MODERATE","409/557",14,{"$nulls":5},"5","247","370","147","235","206","293","0","0","0","0.0751",{"$nulls":20},"0.753036","1.89;1.87;1.91",".;1.155;.","1","-1.15;-1.26;-1.26","0.0;0.002;0.001","0.422;0.456;0.339","0.088;0.073;0.085",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Calcyphosine-2 is a calcium-binding protein with 2 EF-hand motifs (Wang et al., 2002 [PubMed 11846421]).[supplied by OMIM, Mar 2008].",null,null,"0/0","244,0","0","244","0/1","325,29","0.0819","354",null,"chr12:75291815:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0851"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CASP1","chr11:105026847","CASP1(R371C)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense","rs199935430",2.881844380403458E-3,null,"FUNCTION: Thiol protease that cleaves IL-1 beta between an Asp and an Ala, releasing the mature cytokine which is involved in a variety of inflammatory processes. Important for defense against pathogens. Cleaves and activates sterol regulatory element binding proteins (SREBPs). Can also promote apoptosis. Upon inflammasome activation, during DNA virus infection but not RNA virus challenge, controls antiviral immunity through the cleavage of CGAS, rendering it inactive (PubMed:28314590). {ECO:0000269|PubMed:15498465, ECO:0000269|PubMed:1574116, ECO:0000269|PubMed:28314590, ECO:0000269|PubMed:7876192}.; ",{"$nulls":4},"p.Arg371Cys","c.1111C>T","MODERATE","371/404",8,{"$nulls":5},"5","255","372","224","299","206","312","0","0","0","0.1154",{"$nulls":20},"3.066897","4.0;4.0;4.0;4.0;4.0;0.88;0.88;4.0;0.88;0.88",".;.;.;2.68;2.68;.;.;.;.;.","0.999812;0.99915;0.99986;0.99986;0.99986;0.999088;0.999812;0.999088;0.999812;0.999088;0.99986;0.999997","-4.4;-5.13;-4.8;-4.93;-4.93;-5.52;-7.05;-4.59;-7.05;-5.52",".;0.994;0.999;0.997;0.997;1.0;1.0;0.999;1.0;1.0","0.023;0.027;0.035;0.046;0.046;0.028;0.02;0.037;0.02;0.028",".;0.262;0.323;0.264;0.263;0.311;0.281;0.32;0.281;0.312",{"$nulls":3},"1000Gp3_AMR_AF",2.881844380403458E-3,{"$nulls":4},"This gene encodes a protein which is a member of the cysteine-aspartic acid protease (caspase) family. Sequential activation of caspases plays a central role in the execution-phase of cell apoptosis. Caspases exist as inactive proenzymes which undergo proteolytic processing at conserved aspartic residues to produce 2 subunits, large and small, that dimerize to form the active enzyme. This gene was identified by its ability to proteolytically cleave and activate the inactive precursor of interleukin-1, a cytokine involved in the processes such as inflammation, septic shock, and wound healing. This gene has been shown to induce cell apoptosis and may function in various developmental stages. Studies of a similar gene in mouse suggest a role in the pathogenesis of Huntington disease. Alternative splicing results in transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2012].",null,null,"0/0","256,0","0","256","0/1","326,38","0.1044","364",null,"chr11:105026847:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0936"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CBLN2","chr18:72542133","CBLN2(start_lost)",null,null,"signal peptide ","signal-peptide:match_to_sequence_model_evidence_used_in_manual_assertion","MODERATE",null,255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: May play role in synaptogenesis induction. {ECO:0000250}.; ",{"$nulls":4},"p.Met1_Leu9del","c.-12_27delCCACCAGTCCCGATGCAGGCGCCCGGCCGGGGGCCACTC","HIGH","1/224",3,{"$nulls":5},"4","89","75","66","61",null,null,"0","0",{"$nulls":7},"(CBLN2|ENSG00000141668|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","86,0","0","86","0/1","46,24","0.3429","70",null,"chr18:72542133:CGAGTGGCCCCCGGCCGGGCGCCTGCATCGGGACTGGTGG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1967"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CBLN2","chr18:72542133","CBLN2(start_lost)",null,null,"signal peptide ","signal-peptide:match_to_sequence_model_evidence_used_in_manual_assertion","MODERATE",null,255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: May play role in synaptogenesis induction. {ECO:0000250}.; ",{"$nulls":4},"p.Met1_Leu9del","c.-12_27delCCACCAGTCCCGATGCAGGCGCCCGGCCGGGGGCCACTC","HIGH","1/224",3,{"$nulls":5},"4","89","35","66","40",null,null,"0","0",{"$nulls":7},"(CBLN2|ENSG00000141668|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","86,0","0","86","0/1","14,21","0.6","35",null,"chr18:72542133:CGAGTGGCCCCCGGCCGGGCGCCTGCATCGGGACTGGTGG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.35"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CCDC116","chr22:21636457","CCDC116(T410R)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr410Arg","c.1229C>G","MODERATE","410/613",5,{"$nulls":5},"3",null,null,"245","325",{"$nulls":26},"-0.315114","2.75","1.1","1","-1.03",null,"0.08","0.094",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","316,0","0","316","0/1","392,21","0.0508","413",null,"chr22:21636457:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0615"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CCDC142","chr2:74482746","CCDC142(W31L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Trp31Leu","c.92G>T","MODERATE","31/750",1,{"$nulls":5},"4","1038","1329","730","913","947","1199","0","0","0","0.2394",{"$nulls":20},"2.534771","2.8","1.32","1","-1.37;-1.21","0.899","0.043;0.052","0.386;0.385",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1016,0","0","1016","0/1","948,295","0.2373","1243",null,"chr2:74482746:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2333"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CCDC142","chr2:74482746","CCDC142(W31L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Trp31Leu","c.92G>T","MODERATE","31/750",1,{"$nulls":5},"4","1038","898","730","612","947","799","0","0","0","0.4005",{"$nulls":20},"2.534771","2.8","1.32","1","-1.37;-1.21","0.899","0.043;0.052","0.386;0.385",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1019,0","0","1019","0/1","509,346","0.4047","855",null,"chr2:74482746:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3987"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CCDC170","chr6:151538144","CCDC170(S96A)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser96Ala","c.286T>G","MODERATE","96/715",3,{"$nulls":5},"5","156","170","115","107","123","130","0","0","0","0.1462",{"$nulls":20},"2.397522","3.15","1.68","0.787692","-0.83","0.011","0.312","0.25",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","155,0","0","155","0/1","144,23","0.1377","167",null,"chr6:151538144:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1121"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CCDC170","chr6:151538144","CCDC170(S96A)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser96Ala","c.286T>G","MODERATE","96/715",3,{"$nulls":5},"5","156","112","115","78","120","84","0","0","0","0.2857",{"$nulls":20},"2.397522","3.15","1.68","0.787692","-0.83","0.011","0.312","0.25",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","155,0","0","155","0/1","76,31","0.2897","107",null,"chr6:151538144:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3205"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CCL25","chr19:8062223","CCL25(Ter151Rext*?)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Potentially involved in T-cell development. Recombinant protein shows chemotactic activity on thymocytes, macrophages, THP-1 cells, and dendritics cells but is inactive on peripheral blood lymphocytes and neutrophils. Binds to CCR9. Isoform 2 is an antagonist of isoform 1. Binds to atypical chemokine receptor ACKR4 and mediates the recruitment of beta-arrestin (ARRB1/2) to ACKR4.; ",{"$nulls":4},"p.Ter151Argext*?","c.451T>A","HIGH","151/150",5,{"$nulls":5},"3","220","193",null,null,"195","175","0","0","0","0.0514",{"$nulls":20},"0.606001",null,null,"1",{"$nulls":3},"0.072;0.073",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","217,0","0","217","0/1","176,11","0.0588","187",null,"chr19:8062223:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CCT5","chr5:10262500","CCT5(R400Q)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neuropathy, hereditary sensory, with spastic paraplegia, autosomal recessive (HSNSP) [MIM:256840]: A disease characterized by spastic paraplegia and progressive distal sensory neuropathy leading to mutilating ulcerations of the upper and lower limbs. {ECO:0000269|PubMed:16399879}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.; ",{"$nulls":4},"p.Arg400Gln","c.1199G>A","MODERATE","400/541",9,{"$nulls":5},"3",null,null,"571","210","589","231",null,null,"0","0.0519",{"$nulls":20},"3.834785","-2.66","4.04;.;.;.;.","1","-3.86;-3.86;-3.83;-3.86;-3.86","0.822;.;0.997;.;.","0.0","0.896;0.897;0.867;0.868;0.895",{"$nulls":3},"Unknown",-1,"AR","Neuropathy, hereditary sensory, with spastic paraplegia","Neurologic",{"$nulls":3},"C1850395","0/0","691,0","0","691","0/1","242,13","0.051","255",null,"chr5:10262500:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0524"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CDH23","chr10:71807959","CDH23(R2897W)",null,null,"topological domain (Extracellular ), domain (Cadherin 27 ), splice variant (In isoform 10 and isoform 11. ), splice variant (In isoform 5. ), splice variant (In isoform 6. )",{"$nulls":3},255,"PASS","Missense","rs1468886300",-1,"DISEASE: Usher syndrome 1D (USH1D) [MIM:601067]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH1 is characterized by profound congenital sensorineural deafness, absent vestibular function and prepubertal onset of progressive retinitis pigmentosa leading to blindness. {ECO:0000269|PubMed:11138009, ECO:0000269|PubMed:12075507, ECO:0000269|PubMed:15660226, ECO:0000269|PubMed:16679490, ECO:0000269|PubMed:18429043}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Usher syndrome 1D/F (USH1DF) [MIM:601067]: USH1DF patients are heterozygous for mutations in CDH23 and PCDH15, indicating a digenic inheritance pattern. {ECO:0000269|PubMed:15537665}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry.; DISEASE: Deafness, autosomal recessive, 12 (DFNB12) [MIM:601386]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:11090341, ECO:0000269|PubMed:12075507, ECO:0000269|PubMed:12522556, ECO:0000269|PubMed:15829536, ECO:0000269|PubMed:16679490, ECO:0000269|PubMed:17850630, ECO:0000269|PubMed:22899989, ECO:0000269|PubMed:24767429}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pituitary adenoma 5, multiple types (PITA5) [MIM:617540]: A form of pituitary adenoma, a neoplasm of the pituitary gland and one of the most common neuroendocrine tumors. Pituitary adenomas are clinically classified as functional and non-functional tumors, and manifest with a variety of features, including local invasion of surrounding structures and excessive hormone secretion. Functional pituitary adenomas are further classified by the type of hormone they secrete: growth hormone (GH)-secreting, prolactin (PRL)-secreting, adrenocorticotropin (ACTH)-secreting, thyroid- stimulating hormone (TSH)-secreting, and plurihormonal (GH and TSH) tumors. Familial and sporadic forms have been reported. The transmission pattern of familial PITA5 is consistent with autosomal dominant inheritance with reduced penetrance. {ECO:0000269|PubMed:28413019}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells. CDH23 is required for establishing and/or maintaining the proper organization of the stereocilia bundle of hair cells in the cochlea and the vestibule during late embryonic/early postnatal development. It is part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A that mediates mechanotransduction in cochlear hair cells. Required for normal hearing. {ECO:0000269|PubMed:11138009, ECO:0000269|PubMed:16679490}.; ",{"$nulls":4},"p.Arg2897Trp","c.8689C>T","MODERATE","2897/3359",60,{"$nulls":5},"4","663","971","490","692",null,null,"0","0",{"$nulls":22},"4.168817",".;.;.;0.33",".;0.345;.;.","0.537954;0.609095",".;.;.;-2.45",".;0.992;.;.",".;.;.;0.017","0.467;.;0.409;0.363",{"$nulls":3},"Unknown",-1,"AR/Digenic","Deafness, autosomal recessive 12; Usher syndrome, type 1D; Usher syndrome, type 1D /F digenic","Audiologic/Otolaryngologic; Ophthalmologic",null,"This gene is a member of the cadherin superfamily, whose genes encode calcium dependent cell-cell adhesion glycoproteins. The encoded protein is thought to be involved in stereocilia organization and hair bundle formation. The gene is located in a region containing the human deafness loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this cadherin-like gene. Upregulation of this gene may also be associated with breast cancer. Alternative splice variants encoding different isoforms have been described. [provided by RefSeq, May 2013].",null,"C1832394| C4539685| C1832845","0/0","644,0","0","644","0/1","867,55","0.0597","922",null,"chr10:71807959:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0607"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CEL","chr9:133070659","CEL(Splicing Acceptor/Donor Loss)",{"$nulls":6},49.3614,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Catalyzes fat and vitamin absorption. Acts in concert with pancreatic lipase and colipase for the complete digestion of dietary triglycerides.; ",{"$nulls":5},"c.1493+1G>T","HIGH",null,10,{"$nulls":5},"3",null,null,"248","316",{"$nulls":11},"(CEL|ENSG00000170835|1|1.00)",{"$nulls":14},"6.578877",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Maturity-onset diabetes of the young, type 8","Endocrine; Gastrointestinal",{"$nulls":3},"C1853297","0/0","289,0","0","289","0/1","343,19","0.0525","362",null,"chr9:133070659:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0538"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CELF2","chr10:11249186","CELF2(S130G)",null,null,"region of interest (Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of TNNT2 in embryonic, but not adult, skeletal muscle. Activates TNNT2 exon 5 inclusion by antagonizing the repressive effect of PTB. Acts as both an activator and repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Promotes inclusion of exonS 21 and exclusion of exon 5 of the NMDA receptor R1 pre- mRNA. Involved in the apoB RNA editing activity. Increases COX2 mRNA stability and inhibits COX2 mRNA translation in epithelial cells after radiation injury (By similarity). Modulates the cellular apoptosis program by regulating COX2-mediated prostaglandin E2 (PGE2) expression (By similarity). Binds to (CUG)n triplet repeats in the 3'-UTR of transcripts such as DMPK. Binds to the muscle-specific splicing enhancer (MSE) intronic sites flanking the TNNT2 alternative exon 5. Binds preferentially to UG-rich sequences, in particular UG repeat and UGUU motifs. Binds to apoB mRNA, specifically to AU-rich sequences located immediatly upstream of the edited cytidine. Binds AU-rich sequences in the 3'-UTR of COX2 mRNA (By similarity). Binds to an intronic RNA element responsible for the silencing of exon 21 splicing (By similarity). Binds to (CUG)n repeats (By similarity). May be a specific regulator of miRNA biogenesis. Binds to primary microRNA pri-MIR140 and, with CELF1, negatively regulates the processing to mature miRNA (PubMed:28431233). {ECO:0000250|UniProtKB:Q9Z0H4, ECO:0000269|PubMed:11158314, ECO:0000269|PubMed:11577082, ECO:0000269|PubMed:11931771, ECO:0000269|PubMed:12649496, ECO:0000269|PubMed:14973222, ECO:0000269|PubMed:15657417, ECO:0000269|PubMed:15894795, ECO:0000269|PubMed:28431233}.; ",{"$nulls":4},"p.Ser130Gly","c.388A>G","MODERATE","130/533",4,{"$nulls":5},"5","320","234","206","169","293","213","0","0","0","0.1221",{"$nulls":20},"4.029715",".;.;.;0.95;.;.;.;1.29;.;.;0.95;0.95;.;.;.",".;.;.;2.76;2.76;.;.;.;.;.;.;.;.;.;.","1",".;.;.;-3.33;.;.;.;-3.3;.;.;-3.3;-3.33;.;.;-3.3",".;.;.;0.994;0.994;.;0.997;0.997;.;.;.;.;.;.;.",".;.;.;0.0;.;.;.;0.0;.;.;0.0;0.0;.;.;0.0",".;.;.;0.534;0.535;0.539;0.557;0.555;0.538;0.53;0.535;0.535;0.529;0.528;0.525",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","315,0","0","315","0/1","197,29","0.1283","226",null,"chr10:11249186:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1302"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CFHR2","chr1:196958962","CFHR2(R232N)",null,null,"domain (Sushi 4 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in complement regulation. The dimerized forms have avidity for tissue-bound complement fragments and efficiently compete with the physiological complement inhibitor CFH. Can associate with lipoproteins and may play a role in lipid metabolism. {ECO:0000269|PubMed:23487775}.; ",{"$nulls":4},"p.Arg232Asn","c.695_696delGAinsAT","MODERATE","232/270",5,{"$nulls":5},"4","89","105","71","79","70","87","0","0","0","0.1034",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","93,0","0","93","0/1","93,12","0.1143","105",null,"chr1:196958962:GA:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1392"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CFHR2","chr1:196958962","CFHR2(R232N)",null,null,"domain (Sushi 4 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in complement regulation. The dimerized forms have avidity for tissue-bound complement fragments and efficiently compete with the physiological complement inhibitor CFH. Can associate with lipoproteins and may play a role in lipid metabolism. {ECO:0000269|PubMed:23487775}.; ",{"$nulls":4},"p.Arg232Asn","c.695_696delGAinsAT","MODERATE","232/270",5,{"$nulls":5},"5","89","31","71","30","70","28","0","0","0","0.6786",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","93,0","0","93","0/1","11,24","0.6857","35",null,"chr1:196958962:GA:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CFHR4","chr1:196912902","CFHR4(S386*)",null,null,"domain (Sushi 6 ), disulfide bond ",{"$nulls":3},255,"PASS","Loss Of Function","rs760216832",8.6480000000000012E-5,null,"FUNCTION: Involved in complement regulation. Can associate with lipoproteins and may play a role in lipid metabolism.; ","tcga-gbm",{"$nulls":3},"p.Ser386*","c.1157C>G","HIGH","386/577",7,{"$nulls":5},"4","32","35","19","24",null,null,"0","0",{"$nulls":7},"(CFHR4|ENSG00000134365|1|1.00)","(CFHR4|ENSG00000134365|1|1.00)",{"$nulls":13},"7.450335",null,null,"1",{"$nulls":3},"0.155;.;0.138;0.136",{"$nulls":3},"ExAC_AMR_AF",8.6480000000000012E-5,"AD/AR/Digenic","Hemolytic-uremic syndrome, atypical, susceptibility to","Hematologic; Renal",{"$nulls":3},"C2931788","0/0","31,0","0","31","0/1","27,7","0.2059","34",null,"chr1:196912902:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2083"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CHST15","chr10:124021314","CHST15(Q424fs)",null,null,"topological domain (Lumenal )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Sulfotransferase that transfers sulfate from 3'- phosphoadenosine 5'-phosphosulfate (PAPS) to the C-6 hydroxyl group of the GalNAc 4-sulfate residue of chondroitin sulfate A and forms chondroitin sulfate E containing GlcA-GalNAc(4,6-SO(4)) repeating units. It also transfers sulfate to a unique non- reducing terminal sequence, GalNAc(4SO4)-GlcA(2SO4)-GalNAc(6SO4), to yield a highly sulfated structure similar to the structure found in thrombomodulin chondroitin sulfate. May also act as a B- cell receptor involved in BCR ligation-mediated early activation that mediate regulatory signals key to B-cell development and/or regulation of B-cell-specific RAG expression; however such results are unclear in vivo. {ECO:0000269|PubMed:11572857, ECO:0000269|PubMed:12874280}.; ",{"$nulls":4},"p.Gln424fs","c.1272_1288delGCTGTTTGAAAATTGCA","HIGH","424/561",6,{"$nulls":5},"4",null,null,"274","303","311","360",null,null,"0","0.2139",{"$nulls":5},"(CHST15|ENSG00000182022|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","371,0","0","344","0/1","309,85","0.2157","403",null,"chr10:124021314:ATGCAATTTTCAAACAGC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.231"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CHST15","chr10:124021314","CHST15(Q424fs)",null,null,"topological domain (Lumenal )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Sulfotransferase that transfers sulfate from 3'- phosphoadenosine 5'-phosphosulfate (PAPS) to the C-6 hydroxyl group of the GalNAc 4-sulfate residue of chondroitin sulfate A and forms chondroitin sulfate E containing GlcA-GalNAc(4,6-SO(4)) repeating units. It also transfers sulfate to a unique non- reducing terminal sequence, GalNAc(4SO4)-GlcA(2SO4)-GalNAc(6SO4), to yield a highly sulfated structure similar to the structure found in thrombomodulin chondroitin sulfate. May also act as a B- cell receptor involved in BCR ligation-mediated early activation that mediate regulatory signals key to B-cell development and/or regulation of B-cell-specific RAG expression; however such results are unclear in vivo. {ECO:0000269|PubMed:11572857, ECO:0000269|PubMed:12874280}.; ",{"$nulls":4},"p.Gln424fs","c.1272_1288delGCTGTTTGAAAATTGCA","HIGH","424/561",6,{"$nulls":5},"5","344","267","274","194","311","234","0","0","0","0.2692",{"$nulls":5},"(CHST15|ENSG00000182022|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","364,0","0","364","0/1","194,62","0.2422","256",null,"chr10:124021314:ATGCAATTTTCAAACAGC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.232"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CORO7","chr16:4412382","CORO7(R69H)",{"$nulls":6},255,"PASS","Missense","rs147749439",9.1033227127901685E-4,null,"FUNCTION: F-actin regulator involved in anterograde Golgi to endosome transport: upon ubiquitination via 'Lys-33'-linked ubiquitin chains by the BCR(KLHL20) E3 ubiquitin ligase complex, interacts with EPS15 and localizes to the trans-Golgi network, where it promotes actin polymerization, thereby facilitating post- Golgi trafficking. May play a role in the maintenance of the Golgi apparatus morphology. {ECO:0000269|PubMed:16905771, ECO:0000269|PubMed:24768539}.; ",{"$nulls":4},"p.Arg69His","c.206G>A","MODERATE","69/925",3,{"$nulls":5},"5","569","634","391","417","516","570","0","0","0","0.0982",{"$nulls":20},"1.092226","5.0;5.0;-0.27;-0.18;-0.02;-0.02;-1.47;-0.02",".;0.64;0.64;0.64;.;.;.;.","1;1;1;0.999135;0.999949;1",".;-0.09;-0.57;.;.;.;.;.",".;0.0;.;0.0;.;.;.;.",".;0.171;0.161;.;.;.;.;.","0.069;0.071;0.078;0.092;.;.;.;.",{"$nulls":3},"ESP6500_AA_AF",9.1033227127901685E-4,{"$nulls":4},"Coronins, such as CORO7, constitute an evolutionarily conserved family of WD-repeat actin-binding proteins. CORO7 plays a role in Golgi complex morphology and function (Rybakin et al., 2004, 2006 [PubMed 15327992] [PubMed 16905771]).[supplied by OMIM, Mar 2008].",null,null,"0/0","556,0","0","556","0/1","555,62","0.1005","617",null,"chr16:4412382:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1079"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CORO7","chr16:4412382","CORO7(R69H)",{"$nulls":6},255,"PASS","Missense","rs147749439",9.1033227127901685E-4,null,"FUNCTION: F-actin regulator involved in anterograde Golgi to endosome transport: upon ubiquitination via 'Lys-33'-linked ubiquitin chains by the BCR(KLHL20) E3 ubiquitin ligase complex, interacts with EPS15 and localizes to the trans-Golgi network, where it promotes actin polymerization, thereby facilitating post- Golgi trafficking. May play a role in the maintenance of the Golgi apparatus morphology. {ECO:0000269|PubMed:16905771, ECO:0000269|PubMed:24768539}.; ",{"$nulls":4},"p.Arg69His","c.206G>A","MODERATE","69/925",3,{"$nulls":5},"5","569","435","391","300","518","386","0","0","0","0.215",{"$nulls":20},"1.092226","5.0;5.0;-0.27;-0.18;-0.02;-0.02;-1.47;-0.02",".;0.64;0.64;0.64;.;.;.;.","1;1;1;0.999135;0.999949;1",".;-0.09;-0.57;.;.;.;.;.",".;0.0;.;0.0;.;.;.;.",".;0.171;0.161;.;.;.;.;.","0.069;0.071;0.078;0.092;.;.;.;.",{"$nulls":3},"ESP6500_AA_AF",9.1033227127901685E-4,{"$nulls":4},"Coronins, such as CORO7, constitute an evolutionarily conserved family of WD-repeat actin-binding proteins. CORO7 plays a role in Golgi complex morphology and function (Rybakin et al., 2004, 2006 [PubMed 15327992] [PubMed 16905771]).[supplied by OMIM, Mar 2008].",null,null,"0/0","554,0","0","554","0/1","319,89","0.2181","408",null,"chr16:4412382:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2367"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CRNN","chr1:152409760","CRNN(E441G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Survival factor that participates in the clonogenicity of squamous esophageal epithelium cell lines, attenuates deoxycholic acid (DCA)-induced apoptotic cell death and release of calcium. When overexpressed in oral squamous carcinom cell lines, regulates negatively cell proliferation by the induction of G1 arrest. {ECO:0000269|PubMed:15896671, ECO:0000269|PubMed:16640557}.; ",{"$nulls":4},"p.Glu441Gly","c.1322A>G","MODERATE","441/495",3,{"$nulls":5},"4","760","870","584","639","675","776","0","0","0","0.1224",{"$nulls":20},"3.364748","2.98","1.585","0.529757","-1.89","1.0",null,"0.465",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","741,0","0","741","0/1","730,102","0.1226","832",null,"chr1:152409760:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1299"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CRNN","chr1:152409760","CRNN(E441G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Survival factor that participates in the clonogenicity of squamous esophageal epithelium cell lines, attenuates deoxycholic acid (DCA)-induced apoptotic cell death and release of calcium. When overexpressed in oral squamous carcinom cell lines, regulates negatively cell proliferation by the induction of G1 arrest. {ECO:0000269|PubMed:15896671, ECO:0000269|PubMed:16640557}.; ",{"$nulls":4},"p.Glu441Gly","c.1322A>G","MODERATE","441/495",3,{"$nulls":5},"5","760","534","584","390","691","479","0","0","0","0.2589",{"$nulls":20},"3.364748","2.98","1.585","0.529757","-1.89","1.0",null,"0.465",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","743,0","0","743","0/1","373,136","0.2672","509",null,"chr1:152409760:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2487"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CSMD3","chr8:113173871","CSMD3(G187A)",null,null,"topological domain (Extracellular ), domain (Sushi 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in dendrite development. {ECO:0000250|UniProtKB:Q80T79}.; ",{"$nulls":4},"p.Gly187Ala","c.560G>C","MODERATE","187/3707",4,1,{"$nulls":4},"5","434","470","287","328","399","420","0","0","0","0.2357",{"$nulls":20},"1.93092","-0.26",".;2.295;2.295","0.950125;0.950125;0.9347;0.704564","-2.53","0.976;0.1;0.006","0.073;0.055;0.157","0.183;0.177;0.353",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","420,0","0","420","0/1","330,105","0.2414","435",null,"chr8:113173871:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.253"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CSMD3","chr8:113173871","CSMD3(G187A)",null,null,"topological domain (Extracellular ), domain (Sushi 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in dendrite development. {ECO:0000250|UniProtKB:Q80T79}.; ",{"$nulls":4},"p.Gly187Ala","c.560G>C","MODERATE","187/3707",4,1,{"$nulls":4},"5","434","337","287","232","401","295","0","0","0","0.2",{"$nulls":20},"1.93092","-0.26",".;2.295;2.295","0.950125;0.950125;0.9347;0.704564","-2.53","0.976;0.1;0.006","0.073;0.055;0.157","0.183;0.177;0.353",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","426,0","0","426","0/1","255,70","0.2154","325",null,"chr8:113173871:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2284"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CSN3","chr4:70244828","CSN3(S3R)",null,null,"signal peptide ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Kappa-casein stabilizes micelle formation, preventing casein precipitation in milk.; ",{"$nulls":4},"p.Ser3Arg","c.9T>A","MODERATE","3/182",2,{"$nulls":5},"5","265","499","197","353","206","383","0","0","0","0.0627",{"$nulls":20},"0.258723","1.92","1.2","1","-0.49","0.015","0.172","0.223",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","254,0","0","254","0/1","435,28","0.0605","463",null,"chr4:70244828:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0595"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CTBP1","chr4:1238251","CTBP1(P43S)",null,null,"region of interest (Interaction with GLIS2 1 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome (HADDTS) [MIM:617915]: An autosomal dominant disorder characterized by delayed motor development, intellectual disability, failure to thrive, hypotonia, ataxia, and tooth enamel defects. {ECO:0000269|PubMed:27094857}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Corepressor targeting diverse transcription regulators such as GLIS2 or BCL6. Has dehydrogenase activity. Involved in controlling the equilibrium between tubular and stacked structures in the Golgi complex. Functions in brown adipose tissue (BAT) differentiation. {ECO:0000269|PubMed:12419229, ECO:0000269|PubMed:15542832, ECO:0000269|PubMed:18212045, ECO:0000269|PubMed:19103759, ECO:0000269|PubMed:9858600}.; ","level2",{"$nulls":3},"p.Pro43Ser","c.127C>T","MODERATE","43/440",2,{"$nulls":5},"3","720","810",{"$nulls":4},"0.0014","0.0014",{"$nulls":22},"4.066765","0.42",".;1.22;.;.;.;.;.","1","-7.69;-7.69;-7.83;-7.83;-7.83;-7.83;-7.99",".;0.999;.;.;.;.;1.0","0.002;0.002;0.003;0.006;0.004;0.004;0.001","0.568;0.589;.;.;.;.;0.762",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kNOTCH,kWNT",null,null,"C4693578| C1956097","0/0","694,1","0.0014","695","0/1","721,42","0.055","763",null,"chr4:1238251:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CTU1","chr19:51104368","CTU1(A68T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. It is unclear whether it acts as a sulfurtransferase that transfers sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position. {ECO:0000255|HAMAP-Rule:MF_03053, ECO:0000269|PubMed:19017811}.; ",{"$nulls":4},"p.Ala68Thr","c.202G>A","MODERATE","68/348",2,{"$nulls":5},"4","583","514","450","368","508","452","0","0","0","0.2987",{"$nulls":20},"3.600276","2.1","2.7","1","-3.91","1.0","0.003","0.43",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","576,0","0","576","0/1","353,152","0.301","505",null,"chr19:51104368:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2989"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","CTU1","chr19:51104368","CTU1(A68T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). Directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. It is unclear whether it acts as a sulfurtransferase that transfers sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position. {ECO:0000255|HAMAP-Rule:MF_03053, ECO:0000269|PubMed:19017811}.; ",{"$nulls":4},"p.Ala68Thr","c.202G>A","MODERATE","68/348",2,{"$nulls":5},"4","583","284","450","207","507","249","0","0","0","0.7349",{"$nulls":20},"3.600276","2.1","2.7","1","-3.91","1.0","0.003","0.43",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","576,0","0","576","0/1","67,203","0.7519","270",null,"chr19:51104368:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7246"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","CYP4B1","chr1:46818670","CYP4B1(K465N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.; ",{"$nulls":4},"p.Lys465Asn","c.1395G>C","MODERATE","465/512",12,{"$nulls":5},"5","598","565","443","408","492","459","0","0","0","0.159",{"$nulls":20},"2.680986","-0.56",".;4.44;.","0.999739","-4.67;-4.67;-4.66","0.997;0.998;1.0","0.0","0.819;0.747;0.881",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","578,0","0","578","0/1","450,80","0.1509","530",null,"chr1:46818670:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1544"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DDRGK1","chr20:3200034","DDRGK1(E159D)",null,null,"region of interest (Mediates interaction with TRIP4 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Spondyloepimetaphyseal dysplasia, Shohat type (SEMDSH) [MIM:602557]: An autosomal recessive skeletal dysplasia that affects cartilage development. It is characterized by vertebral, epiphyseal, and metaphyseal abnormalities, including scoliosis with vertebral compression fractures, flattened vertebral bodies, and hypomineralization of long bones. Affected individuals may exhibit a small trunk, short neck, small limbs, joint laxity, bowlegs, and/or abdominal distension with hepatosplenomegaly. {ECO:0000269|PubMed:28263186}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Protein which interacts with the E3 UFM1-protein ligase UFL1 and one of its substrates TRIP4 and is required for TRIP4 ufmylation. Through TRIP4 ufmylation may regulate nuclear receptors-mediated transcription (PubMed:25219498). May play a role in NF-kappa-B-mediated transcription through regulation of the phosphorylation and the degradation of NFKBIA, the inhibitor of NF-kappa-B (PubMed:23675531). May also play a role in the cellular response to endoplasmic reticulum stress (By similarity). Plays a role in cartilage development through SOX9, inhibiting the ubiquitin-mediated proteasomal degradation of this transcriptional regulator (PubMed:28263186). {ECO:0000250|UniProtKB:Q80WW9, ECO:0000269|PubMed:23675531, ECO:0000269|PubMed:25219498, ECO:0000269|PubMed:28263186}.; ",{"$nulls":4},"p.Glu159Asp","c.477G>T","MODERATE","159/314",4,{"$nulls":5},"5","207","127","170","98","154","90","0","0","0","0.0889",{"$nulls":20},"2.20875","0.82;.","2.045;.","0.999558","-2.2;-1.99","0.992;.","0.076;0.169","0.475;0.469",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1865185","0/0","205,0","0","205","0/1","112,10","0.082","122",null,"chr20:3200034:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0816"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DMXL2","chr15:51536735","DMXL2(E582V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Polyendocrine-polyneuropathy syndrome (PEPNS) [MIM:616113]: A progressive endocrine and neurodevelopmental disorder manifesting early in childhood with growth retardation and recurrent episodes of profound asymptomatic hypoglycemia. PEPNS is characterized by central hypothyroidism, hypogonadotropic hypogonadism, incomplete puberty, progressive non-autoimmune insulin-dependent diabetes mellitus, peripheral demyelinating sensorimotor polyneuropathy, and cerebellar and pyramidal signs. {ECO:0000269|PubMed:25248098}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Deafness, autosomal dominant, 71 (DFNA71) [MIM:617605]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA71 is characterized by bilateral mild to moderate hearing loss before age 20 years, which gradually progresses to severe to profound hearing loss. {ECO:0000269|PubMed:27657680}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May serve as a scaffold protein for MADD and RAB3GA on synaptic vesicles (PubMed:11809763). Plays a role in the brain as a key controller of neuronal and endocrine homeostatic processes (By similarity). {ECO:0000250|UniProtKB:Q8BPN8, ECO:0000269|PubMed:11809763}.; ",{"$nulls":4},"p.Glu582Val","c.1745A>T","MODERATE","582/3037",12,{"$nulls":5},"4","775","900","575","631","720","832","0","0","0","0.2536",{"$nulls":20},"1.447093","1.96;1.96;1.81","1.04","1","-2.42;-2.42;-2.4","0.006;.;.","0.229;0.23;0.161","0.408;0.469;0.436",{"$nulls":3},"Unknown",-1,"AR","Polyendocrine-polyneuropathy syndrome","Endocrine; Neurologic",{"$nulls":3},"C5231450| C4539881| C4015261","0/0","763,0","0","763","0/1","643,220","0.2549","863",null,"chr15:51536735:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2583"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DMXL2","chr15:51536735","DMXL2(E582V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Polyendocrine-polyneuropathy syndrome (PEPNS) [MIM:616113]: A progressive endocrine and neurodevelopmental disorder manifesting early in childhood with growth retardation and recurrent episodes of profound asymptomatic hypoglycemia. PEPNS is characterized by central hypothyroidism, hypogonadotropic hypogonadism, incomplete puberty, progressive non-autoimmune insulin-dependent diabetes mellitus, peripheral demyelinating sensorimotor polyneuropathy, and cerebellar and pyramidal signs. {ECO:0000269|PubMed:25248098}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Deafness, autosomal dominant, 71 (DFNA71) [MIM:617605]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. DFNA71 is characterized by bilateral mild to moderate hearing loss before age 20 years, which gradually progresses to severe to profound hearing loss. {ECO:0000269|PubMed:27657680}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May serve as a scaffold protein for MADD and RAB3GA on synaptic vesicles (PubMed:11809763). Plays a role in the brain as a key controller of neuronal and endocrine homeostatic processes (By similarity). {ECO:0000250|UniProtKB:Q8BPN8, ECO:0000269|PubMed:11809763}.; ",{"$nulls":4},"p.Glu582Val","c.1745A>T","MODERATE","582/3037",12,{"$nulls":5},"4","775","521","575","384","719","463","0","0","0","0.4989",{"$nulls":20},"1.447093","1.96;1.96;1.81","1.04","1","-2.42;-2.42;-2.4","0.006;.;.","0.229;0.23;0.161","0.408;0.469;0.436",{"$nulls":3},"Unknown",-1,"AR","Polyendocrine-polyneuropathy syndrome","Endocrine; Neurologic",{"$nulls":3},"C5231450| C4539881| C4015261","0/0","763,0","0","763","0/1","250,252","0.502","502",null,"chr15:51536735:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.513"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DNAH10","chr12:123841323","DNAH10(M1656T)",null,null,"region of interest (Stem ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs968539132",-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Involved in sperm motility; implicated in sperm flagellar assembly (By similarity). Probable inner arm dynein heavy chain. {ECO:0000250}.; ",{"$nulls":4},"p.Met1656Thr","c.4967T>C","MODERATE","1656/4532",29,{"$nulls":5},"5","110","124","101","111","89","99","0","0","0","0.2828",{"$nulls":20},"3.916011",null,".;3.39","1",null,".;0.998",{"$nulls":5},"Unknown",-1,{"$nulls":7},"0/0","108,0","0","108","0/1","94,28","0.2295","122",null,"chr12:123841323:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2252"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DNAH10","chr12:123841323","DNAH10(M1656T)",null,null,"region of interest (Stem ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs968539132",-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Involved in sperm motility; implicated in sperm flagellar assembly (By similarity). Probable inner arm dynein heavy chain. {ECO:0000250}.; ",{"$nulls":4},"p.Met1656Thr","c.4967T>C","MODERATE","1656/4532",29,{"$nulls":5},"5","110","128","101","112","89","93","0","0","0","0.3763",{"$nulls":20},"3.916011",null,".;3.39","1",null,".;0.998",{"$nulls":5},"Unknown",-1,{"$nulls":7},"0/0","106,0","0","106","0/1","87,41","0.3203","128",null,"chr12:123841323:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3214"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DNAH9","chr17:11608297","DNAH9(E196Q)",null,null,"region of interest (Stem ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.; ",{"$nulls":4},"p.Glu196Gln","c.586G>C","MODERATE","196/4486",2,{"$nulls":5},"5","354","349","246","232","323","327","0","0","0","0.1223",{"$nulls":20},"1.650128","1.73;1.35;1.69","1.935;.;.","1","-1.41;.;-1.46","0.004;.;0.007","0.157;.;0.179","0.133;0.075;0.118",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4749028","0/0","352,0","0","352","0/1","297,47","0.1366","344",null,"chr17:11608297:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1336"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DNAH9","chr17:11608297","DNAH9(E196Q)",null,null,"region of interest (Stem ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.; ",{"$nulls":4},"p.Glu196Gln","c.586G>C","MODERATE","196/4486",2,{"$nulls":5},"5","354","156","246","98","325","139","0","0","0","0.3597",{"$nulls":20},"1.650128","1.73;1.35;1.69","1.935;.;.","1","-1.41;.;-1.46","0.004;.;0.007","0.157;.;0.179","0.133;0.075;0.118",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4749028","0/0","350,0","0","350","0/1","97,55","0.3618","152",null,"chr17:11608297:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3878"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DNAJC30","chr7:73683072","DNAJC30(E118*)",null,null,"helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Glu118*","c.352G>T","HIGH","118/226",1,{"$nulls":5},"3",null,null,"577","619","540","598",null,null,"0","0.0552",{"$nulls":20},"7.047782",null,null,"1",{"$nulls":3},"0.055",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","685,0","0","685","0/1","695,38","0.0518","734",null,"chr7:73683072:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0533"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DOCK8","chr9:311963","DOCK8(R180C)",{"$nulls":6},255,"PASS","Missense","rs141961156",1.5128593040847202E-3,"DISEASE: Hyperimmunoglobulin E recurrent infection syndrome, autosomal recessive (AR-HIES) [MIM:243700]: A rare disorder characterized by immunodeficiency, recurrent infections, eczema, increased serum IgE, eosinophilia and lack of connective tissue and skeletal involvement. {ECO:0000269|PubMed:19776401}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 2 (MRD2) [MIM:614113]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:18060736}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration disrupting DOCK8 has been found in a patient with mental retardation and ectodermal dysplasia. A balanced translocation, t(X;9) (q13.1;p24). A genomic deletion of approximately 230 kb in subtelomeric 9p has been detected in a patient with mental retardation.; ","FUNCTION: Guanine nucleotide exchange factor (GEF) which specifically activates small GTPase CDC42 by exchanging bound GDP for free GTP (PubMed:28028151, PubMed:22461490). During immune responses, required for interstitial dendritic cell (DC) migration by locally activating CDC42 at the leading edge membrane of DC (By similarity). Required for CD4(+) T-cell migration in response to chemokine stimulation by promoting CDC42 activation at T cell leading edge membrane (PubMed:28028151). Is involved in NK cell cytotoxicity by controlling polarization of microtubule-organizing center (MTOC), and possibly regulating CCDC88B-mediated lytic granule transport to MTOC during cell killing (PubMed:25762780). {ECO:0000250|UniProtKB:Q8C147, ECO:0000269|PubMed:22461490, ECO:0000269|PubMed:25762780, ECO:0000269|PubMed:28028151}.; ",{"$nulls":4},"p.Arg180Cys","c.538C>T","MODERATE","180/2099",6,1,{"$nulls":4},"5","245","366","198","293","221","316","0","0","0","0.3259",{"$nulls":20},"1.169254",".;.;2.54","1.78;.;.","0.927475;0.927475;0.84562",".;.;-2.78","0.032;.;.",".;.;0.027","0.213;0.211;0.232",{"$nulls":3},"1000Gp3_AFR_AF",1.5128593040847202E-3,"AR","Hyper-IgE recurrent infection syndrome, autosomal recessive","Allergy/Immunology/Infectious; Neurologic; Oncologic",{"$nulls":3},"C4722305","0/0","243,1","0.0041","244","0/1","239,115","0.3249","354",null,"chr9:311963:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3174"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DOCK8","chr9:311963","DOCK8(R180C)",{"$nulls":6},255,"PASS","Missense","rs141961156",1.5128593040847202E-3,"DISEASE: Hyperimmunoglobulin E recurrent infection syndrome, autosomal recessive (AR-HIES) [MIM:243700]: A rare disorder characterized by immunodeficiency, recurrent infections, eczema, increased serum IgE, eosinophilia and lack of connective tissue and skeletal involvement. {ECO:0000269|PubMed:19776401}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 2 (MRD2) [MIM:614113]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:18060736}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration disrupting DOCK8 has been found in a patient with mental retardation and ectodermal dysplasia. A balanced translocation, t(X;9) (q13.1;p24). A genomic deletion of approximately 230 kb in subtelomeric 9p has been detected in a patient with mental retardation.; ","FUNCTION: Guanine nucleotide exchange factor (GEF) which specifically activates small GTPase CDC42 by exchanging bound GDP for free GTP (PubMed:28028151, PubMed:22461490). During immune responses, required for interstitial dendritic cell (DC) migration by locally activating CDC42 at the leading edge membrane of DC (By similarity). Required for CD4(+) T-cell migration in response to chemokine stimulation by promoting CDC42 activation at T cell leading edge membrane (PubMed:28028151). Is involved in NK cell cytotoxicity by controlling polarization of microtubule-organizing center (MTOC), and possibly regulating CCDC88B-mediated lytic granule transport to MTOC during cell killing (PubMed:25762780). {ECO:0000250|UniProtKB:Q8C147, ECO:0000269|PubMed:22461490, ECO:0000269|PubMed:25762780, ECO:0000269|PubMed:28028151}.; ",{"$nulls":4},"p.Arg180Cys","c.538C>T","MODERATE","180/2099",6,1,{"$nulls":4},"5","245","302","198","239","219","262","0","0","0","0.5954",{"$nulls":20},"1.169254",".;.;2.54","1.78;.;.","0.927475;0.927475;0.84562",".;.;-2.78","0.032;.;.",".;.;0.027","0.213;0.211;0.232",{"$nulls":3},"1000Gp3_AFR_AF",1.5128593040847202E-3,"AR","Hyper-IgE recurrent infection syndrome, autosomal recessive","Allergy/Immunology/Infectious; Neurologic; Oncologic",{"$nulls":3},"C4722305","0/0","243,1","0.0041","244","0/1","136,164","0.5467","300",null,"chr9:311963:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5816"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DOCK8","chr9:334265","DOCK8(F390del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,"DISEASE: Hyperimmunoglobulin E recurrent infection syndrome, autosomal recessive (AR-HIES) [MIM:243700]: A rare disorder characterized by immunodeficiency, recurrent infections, eczema, increased serum IgE, eosinophilia and lack of connective tissue and skeletal involvement. {ECO:0000269|PubMed:19776401}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 2 (MRD2) [MIM:614113]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:18060736}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration disrupting DOCK8 has been found in a patient with mental retardation and ectodermal dysplasia. A balanced translocation, t(X;9) (q13.1;p24). A genomic deletion of approximately 230 kb in subtelomeric 9p has been detected in a patient with mental retardation.; ","FUNCTION: Guanine nucleotide exchange factor (GEF) which specifically activates small GTPase CDC42 by exchanging bound GDP for free GTP (PubMed:28028151, PubMed:22461490). During immune responses, required for interstitial dendritic cell (DC) migration by locally activating CDC42 at the leading edge membrane of DC (By similarity). Required for CD4(+) T-cell migration in response to chemokine stimulation by promoting CDC42 activation at T cell leading edge membrane (PubMed:28028151). Is involved in NK cell cytotoxicity by controlling polarization of microtubule-organizing center (MTOC), and possibly regulating CCDC88B-mediated lytic granule transport to MTOC during cell killing (PubMed:25762780). {ECO:0000250|UniProtKB:Q8C147, ECO:0000269|PubMed:22461490, ECO:0000269|PubMed:25762780, ECO:0000269|PubMed:28028151}.; ",{"$nulls":4},"p.Phe390del","c.1169_1171delTCT","MODERATE","390/2099",11,{"$nulls":5},"4","469","728","383","585","411","647","0","0","0","0.0974",{"$nulls":31},"Unknown",-1,"AR","Hyper-IgE recurrent infection syndrome, autosomal recessive","Allergy/Immunology/Infectious; Neurologic; Oncologic",{"$nulls":3},"C4722305","0/0","457,0","0","457","0/1","616,65","0.0954","681",null,"chr9:334265:CCTT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0974"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DOCK8","chr9:334265","DOCK8(F390del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,"DISEASE: Hyperimmunoglobulin E recurrent infection syndrome, autosomal recessive (AR-HIES) [MIM:243700]: A rare disorder characterized by immunodeficiency, recurrent infections, eczema, increased serum IgE, eosinophilia and lack of connective tissue and skeletal involvement. {ECO:0000269|PubMed:19776401}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 2 (MRD2) [MIM:614113]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:18060736}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration disrupting DOCK8 has been found in a patient with mental retardation and ectodermal dysplasia. A balanced translocation, t(X;9) (q13.1;p24). A genomic deletion of approximately 230 kb in subtelomeric 9p has been detected in a patient with mental retardation.; ","FUNCTION: Guanine nucleotide exchange factor (GEF) which specifically activates small GTPase CDC42 by exchanging bound GDP for free GTP (PubMed:28028151, PubMed:22461490). During immune responses, required for interstitial dendritic cell (DC) migration by locally activating CDC42 at the leading edge membrane of DC (By similarity). Required for CD4(+) T-cell migration in response to chemokine stimulation by promoting CDC42 activation at T cell leading edge membrane (PubMed:28028151). Is involved in NK cell cytotoxicity by controlling polarization of microtubule-organizing center (MTOC), and possibly regulating CCDC88B-mediated lytic granule transport to MTOC during cell killing (PubMed:25762780). {ECO:0000250|UniProtKB:Q8C147, ECO:0000269|PubMed:22461490, ECO:0000269|PubMed:25762780, ECO:0000269|PubMed:28028151}.; ",{"$nulls":4},"p.Phe390del","c.1169_1171delTCT","MODERATE","390/2099",11,{"$nulls":5},"4","469","603","383","467","412","544","0","0","0","0.2629",{"$nulls":31},"Unknown",-1,"AR","Hyper-IgE recurrent infection syndrome, autosomal recessive","Allergy/Immunology/Infectious; Neurologic; Oncologic",{"$nulls":3},"C4722305","0/0","457,0","0","457","0/1","411,150","0.2674","561",null,"chr9:334265:CCTT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2719"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DPY19L3","chr19:32480495","DPY19L3(Y643H)",{"$nulls":6},255,"PASS","Missense","rs764065539",1.217E-4,null,"FUNCTION: Probable C-mannosyltransferase that mediates C- mannosylation of tryptophan residues on target proteins. {ECO:0000250}.; ",{"$nulls":4},"p.Tyr643His","c.1927T>C","MODERATE","643/716",18,{"$nulls":5},"4","583","440","405","298","542","402","0.0017","0.0017","0","0.0821",{"$nulls":20},"2.549774","0.54","2.11;.;2.11","0.998745","-1.3;.;-1.3","0.011;.;0.011","0.391;.;0.391","0.454;0.452;0.454",{"$nulls":3},"ExAC_SAS_AF",1.217E-4,{"$nulls":7},"0/0","554,1","0.0018","555","0/1","359,34","0.0865","393",null,"chr19:32480495:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0906"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DRD3","chr3:114139616","DRD3(V203L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Tremor, hereditary essential 1 (ETM1) [MIM:190300]: A common movement disorder mainly characterized by postural tremor of the arms. Head, legs, trunk, voice, jaw, and facial muscles also may be involved. The condition can be aggravated by emotions, hunger, fatigue and temperature extremes, and may cause a functional disability or even incapacitation. Inheritance is autosomal dominant. {ECO:0000269|PubMed:16650084, ECO:0000269|PubMed:16809426}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:1362221, ECO:0000269|PubMed:9514583}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; ","FUNCTION: Dopamine receptor whose activity is mediated by G proteins which inhibit adenylyl cyclase. Promotes cell proliferation. {ECO:0000269|PubMed:19520868}.; ",{"$nulls":4},"p.Val203Leu","c.607G>T","MODERATE","203/400",5,{"$nulls":5},"3","244","409",{"$nulls":4},"0","0",{"$nulls":22},"1.95084","1.27",null,"0.99999","-1.7;-1.7;-1.63;-1.7",".;.;0.653;.","0.006;0.006;0.293;0.006","0.59;0.578;0.637;0.579",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1860861| C0036341","0/0","243,0","0","243","0/1","383,21","0.052","404",null,"chr3:114139616:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DTNB","chr2:25455460","DTNB(A372S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala372Ser","c.1114G>T","MODERATE","372/627",11,{"$nulls":5},"4","584","777","411","515","507","687","0","0","0","0.0611",{"$nulls":20},"2.000045","2.18;2.2;2.18;2.2;2.17",".;1.07;1.07;1.07;.","1;1;1;0.590384;0.590384;0.590384;0.590384;0.590384;0.590384","-0.59;-0.59;-0.39;-0.59;-0.39",".;0.228;0.082;.;0.049","0.701;0.681;0.667;0.673;0.646","0.316;0.342;0.342;0.261;0.308",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","551,0","0","551","0/1","695,44","0.0595","739",null,"chr2:25455460:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0621"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","DYNC1H1","chr14:101983221","DYNC1H1(L388F)",null,null,"region of interest (Stem ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Charcot-Marie-Tooth disease 2O (CMT2O) [MIM:614228]: An axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. {ECO:0000269|PubMed:21820100, ECO:0000269|PubMed:24307404, ECO:0000269|PubMed:25512093}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 13 (MRD13) [MIM:614563]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD13 is associated with variable neuronal migration defects and mild dysmorphic features. Some patients may also show signs of peripheral neuropathy, such as abnormal gait and hyporeflexia. {ECO:0000269|PubMed:21076407, ECO:0000269|PubMed:22368300, ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23603762, ECO:0000269|PubMed:28193117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant (SMALED1) [MIM:158600]: A form of spinal muscular atrophy, a neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMALED1 is characterized by muscle weakness predominantly affecting the proximal lower extremities. {ECO:0000269|PubMed:22459677, ECO:0000269|PubMed:22847149, ECO:0000269|PubMed:25484024, ECO:0000269|PubMed:25512093, ECO:0000269|PubMed:26846447, ECO:0000269|PubMed:28193117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Plays a role in mitotic spindle assembly and metaphase plate congression (PubMed:27462074). {ECO:0000269|PubMed:27462074}.; ",{"$nulls":4},"p.Leu388Phe","c.1164G>C","MODERATE","388/4646",6,{"$nulls":5},"5","396","576","311","444","336","507","0","0","0","0.1992",{"$nulls":20},"3.4247","-0.15","2.64","1","-3.07","0.996","0.034","0.794",{"$nulls":3},"Unknown",-1,"AD","Charcot-Marie-Tooth disease, axonal, type 2O; Mental retardation, autosomal dominant 13; Spinal muscular atrophy, lower extremity, autosomal dominant ","Musculoskeletal; Neurologic",{"$nulls":3},"C1834690| C3281202| C3280220","0/0","389,0","0","389","0/1","447,114","0.2032","561",null,"chr14:101983221:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2072"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","DYNC1H1","chr14:101983221","DYNC1H1(L388F)",null,null,"region of interest (Stem ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Charcot-Marie-Tooth disease 2O (CMT2O) [MIM:614228]: An axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. {ECO:0000269|PubMed:21820100, ECO:0000269|PubMed:24307404, ECO:0000269|PubMed:25512093}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 13 (MRD13) [MIM:614563]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD13 is associated with variable neuronal migration defects and mild dysmorphic features. Some patients may also show signs of peripheral neuropathy, such as abnormal gait and hyporeflexia. {ECO:0000269|PubMed:21076407, ECO:0000269|PubMed:22368300, ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23603762, ECO:0000269|PubMed:28193117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Spinal muscular atrophy, lower extremity-predominant 1, autosomal dominant (SMALED1) [MIM:158600]: A form of spinal muscular atrophy, a neuromuscular disorder characterized by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMALED1 is characterized by muscle weakness predominantly affecting the proximal lower extremities. {ECO:0000269|PubMed:22459677, ECO:0000269|PubMed:22847149, ECO:0000269|PubMed:25484024, ECO:0000269|PubMed:25512093, ECO:0000269|PubMed:26846447, ECO:0000269|PubMed:28193117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Plays a role in mitotic spindle assembly and metaphase plate congression (PubMed:27462074). {ECO:0000269|PubMed:27462074}.; ",{"$nulls":4},"p.Leu388Phe","c.1164G>C","MODERATE","388/4646",6,{"$nulls":5},"5","396","382","311","297","336","338","0","0","0","0.3373",{"$nulls":20},"3.4247","-0.15","2.64","1","-3.07","0.996","0.034","0.794",{"$nulls":3},"Unknown",-1,"AD","Charcot-Marie-Tooth disease, axonal, type 2O; Mental retardation, autosomal dominant 13; Spinal muscular atrophy, lower extremity, autosomal dominant ","Musculoskeletal; Neurologic",{"$nulls":3},"C1834690| C3281202| C3280220","0/0","389,0","0","389","0/1","248,129","0.3422","377",null,"chr14:101983221:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3569"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","EGR2","chr10:62815885","EGR2(D49H)",null,null,"splice variant (In isoform Short. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neuropathy, congenital hypomyelinating or amyelinating (CHN) [MIM:605253]: A severe degenerating neuropathy that results from a congenital impairment in myelin formation. It is clinically characterized by early onset of hypotonia, areflexia, distal muscle weakness, and very slow nerve conduction velocities (as low as 3m/s). Some patients manifest nearly complete absence of spontaneous limb movements, respiratory distress at birth, and complete absence of myelin shown by electron microscopy of peripheral nerves. Inheritance can be autosomal dominant or recessive. {ECO:0000269|PubMed:22522483, ECO:0000269|PubMed:9537424}. Note=The disease is caused by mutations affecting the gene represented in this entry. Patients affected by the amyelinating form carry a causative, homozygous deletion encompassing a myelin-specific enhancer of EGR2 (PubMed:22522483). {ECO:0000269|PubMed:22522483}.; DISEASE: Charcot-Marie-Tooth disease 1D (CMT1D) [MIM:607678]: A dominant demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. {ECO:0000269|PubMed:10502832, ECO:0000269|PubMed:10762521, ECO:0000269|PubMed:11239949, ECO:0000269|PubMed:12736090, ECO:0000269|PubMed:15241803, ECO:0000269|PubMed:15947997, ECO:0000269|PubMed:9537424, ECO:0000269|Ref.15}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dejerine-Sottas syndrome (DSS) [MIM:145900]: A severe degenerating neuropathy of the demyelinating Charcot-Marie-Tooth disease category, with onset by age 2 years. Characterized by motor and sensory neuropathy with very slow nerve conduction velocities, increased cerebrospinal fluid protein concentrations, hypertrophic nerve changes, delayed age of walking as well as areflexia. There are both autosomal dominant and autosomal recessive forms of Dejerine-Sottas syndrome. {ECO:0000269|PubMed:10371530}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sequence-specific DNA-binding transcription factor. Binds to two specific DNA sites located in the promoter region of HOXA4. {ECO:0000269|PubMed:21836637}.; ",{"$nulls":4},"p.Asp49His","c.145G>C","MODERATE","49/476",1,{"$nulls":5},"5","216","302","174","260","159","237","0","0","0","0.2321",{"$nulls":20},"3.862467","2.56;2.56;.","1.095;1.095;.","0.998004;0.998004;1","-1.28;-1.28;.","0.978;0.978;.","0.003;0.003;.","0.489;0.454;.",{"$nulls":3},"Unknown",-1,"AD/AR","Charcot-Marie-Tooth disease, demyelinating, type 1D; Neuropathy, congenital hypomyelinating, 1 ; Dejerine-Sottas disease","Neurologic",{"$nulls":3},"C4721436| C0011195| C1843247","0/0","212,0","0","212","0/1","238,58","0.1959","296",null,"chr10:62815885:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","EGR2","chr10:62815885","EGR2(D49H)",null,null,"splice variant (In isoform Short. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Neuropathy, congenital hypomyelinating or amyelinating (CHN) [MIM:605253]: A severe degenerating neuropathy that results from a congenital impairment in myelin formation. It is clinically characterized by early onset of hypotonia, areflexia, distal muscle weakness, and very slow nerve conduction velocities (as low as 3m/s). Some patients manifest nearly complete absence of spontaneous limb movements, respiratory distress at birth, and complete absence of myelin shown by electron microscopy of peripheral nerves. Inheritance can be autosomal dominant or recessive. {ECO:0000269|PubMed:22522483, ECO:0000269|PubMed:9537424}. Note=The disease is caused by mutations affecting the gene represented in this entry. Patients affected by the amyelinating form carry a causative, homozygous deletion encompassing a myelin-specific enhancer of EGR2 (PubMed:22522483). {ECO:0000269|PubMed:22522483}.; DISEASE: Charcot-Marie-Tooth disease 1D (CMT1D) [MIM:607678]: A dominant demyelinating form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Demyelinating neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. {ECO:0000269|PubMed:10502832, ECO:0000269|PubMed:10762521, ECO:0000269|PubMed:11239949, ECO:0000269|PubMed:12736090, ECO:0000269|PubMed:15241803, ECO:0000269|PubMed:15947997, ECO:0000269|PubMed:9537424, ECO:0000269|Ref.15}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Dejerine-Sottas syndrome (DSS) [MIM:145900]: A severe degenerating neuropathy of the demyelinating Charcot-Marie-Tooth disease category, with onset by age 2 years. Characterized by motor and sensory neuropathy with very slow nerve conduction velocities, increased cerebrospinal fluid protein concentrations, hypertrophic nerve changes, delayed age of walking as well as areflexia. There are both autosomal dominant and autosomal recessive forms of Dejerine-Sottas syndrome. {ECO:0000269|PubMed:10371530}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Sequence-specific DNA-binding transcription factor. Binds to two specific DNA sites located in the promoter region of HOXA4. {ECO:0000269|PubMed:21836637}.; ",{"$nulls":4},"p.Asp49His","c.145G>C","MODERATE","49/476",1,{"$nulls":5},"5","216","214","174","180","158","171","0","0","0","0.3333",{"$nulls":20},"3.862467","2.56;2.56;.","1.095;1.095;.","0.998004;0.998004;1","-1.28;-1.28;.","0.978;0.978;.","0.003;0.003;.","0.489;0.454;.",{"$nulls":3},"Unknown",-1,"AD/AR","Charcot-Marie-Tooth disease, demyelinating, type 1D; Neuropathy, congenital hypomyelinating, 1 ; Dejerine-Sottas disease","Neurologic",{"$nulls":3},"C4721436| C0011195| C1843247","0/0","210,0","0","210","0/1","148,64","0.3019","212",null,"chr10:62815885:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3222"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","EME2","chr16:1775653","EME2(V250F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Interacts with MUS81 to form a DNA structure-specific endonuclease which cleaves substrates such as 3'-flap structures. {ECO:0000269|PubMed:17289582}.; ",{"$nulls":4},"p.Val250Phe","c.748G>T","MODERATE","250/379",6,{"$nulls":5},"4","591","692",null,null,"460","529","0","0","0","0.0643",{"$nulls":20},"-0.473721",null,"-1.99","1","2.23",null,"1.0","0.305",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","586,0","0","586","0/1","636,35","0.0522","671",null,"chr16:1775653:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ENAH","chr1:225519566","ENAH(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss","rs752410405",-1,null,"FUNCTION: Ena/VASP proteins are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance and lamellipodial and filopodial dynamics in migrating cells. ENAH induces the formation of F-actin rich outgrowths in fibroblasts. Acts synergistically with BAIAP2-alpha and downstream of NTN1 to promote filipodia formation (By similarity). {ECO:0000250, ECO:0000269|PubMed:11696321, ECO:0000269|PubMed:18158903}.; ",{"$nulls":5},"c.447-1G>C","HIGH",null,5,{"$nulls":5},"5","121","113","84","66","106","81","0","0","0","0.1605",{"$nulls":5},"(ENAH|ENSG00000154380|1|1.00)",{"$nulls":14},"5.786691",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","112,0","0","112","0/1","69,27","0.2812","96",null,"chr1:225519566:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2273"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ENAH","chr1:225519566","ENAH(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss","rs752410405",-1,null,"FUNCTION: Ena/VASP proteins are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance and lamellipodial and filopodial dynamics in migrating cells. ENAH induces the formation of F-actin rich outgrowths in fibroblasts. Acts synergistically with BAIAP2-alpha and downstream of NTN1 to promote filipodia formation (By similarity). {ECO:0000250, ECO:0000269|PubMed:11696321, ECO:0000269|PubMed:18158903}.; ",{"$nulls":5},"c.447-1G>C","HIGH",null,5,{"$nulls":5},"5","121","103","84","59","106","58","0","0","0","0.1724",{"$nulls":5},"(ENAH|ENSG00000154380|1|1.00)",{"$nulls":14},"5.786691",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","111,0","0","111","0/1","54,29","0.3494","83",null,"chr1:225519566:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.322"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","EVC2","chr4:5708362","EVC2(R40_P50del)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,"DISEASE: Acrofacial dysostosis, Weyers type (WAD) [MIM:193530]: An autosomal dominant condition characterized by dysplastic nails, postaxial polydactyly, dental anomalies, short limbs, short stature and normal intelligence. The phenotype is milder than Ellis-van Creveld syndrome. {ECO:0000269|PubMed:16404586}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. Plays a critical role in bone formation and skeletal development. May be involved in early embryonic morphogenesis. {ECO:0000250|UniProtKB:Q8K1G2}.; ",{"$nulls":4},"p.Arg40_Pro50del","c.119_151delGCCCCCTCGGCGCGCAGCCACCCCGGGATCCCC","MODERATE","40/1308",1,{"$nulls":5},"5","210","191","156","141","149","157","0","0","0","0.3439",{"$nulls":31},"Unknown",-1,"AD/AR","Ellis-van Creveld syndrome; Weyers acrodental dysostosis","Cardiovascular; Craniofacial; Dental; Dermatologic; Musculoskeletal",null,"This gene encodes a protein that functions in bone formation and skeletal development. Mutations in this gene, as well as in a neighboring gene that lies in a head-to-head configuration, cause Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia that is also known as chondroectodermal dysplasia. Mutations in this gene also cause acrofacial dysostosis Weyers type, also referred to as Curry-Hall syndrome, a disease that combines limb and facial abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009].",null,"C0013903| C0457013","0/0","246,0","0","246","0/1","143,62","0.3024","205",null,"chr4:5708362:TGGGGATCCCGGGGTGGCTGCGCGCCGAGGGGGC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3262"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","EVC2","chr4:5708362","EVC2(R40_P50del)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,"DISEASE: Acrofacial dysostosis, Weyers type (WAD) [MIM:193530]: An autosomal dominant condition characterized by dysplastic nails, postaxial polydactyly, dental anomalies, short limbs, short stature and normal intelligence. The phenotype is milder than Ellis-van Creveld syndrome. {ECO:0000269|PubMed:16404586}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of the EvC complex that positively regulates ciliary Hedgehog (Hh) signaling. Plays a critical role in bone formation and skeletal development. May be involved in early embryonic morphogenesis. {ECO:0000250|UniProtKB:Q8K1G2}.; ",{"$nulls":4},"p.Arg40_Pro50del","c.119_151delGCCCCCTCGGCGCGCAGCCACCCCGGGATCCCC","MODERATE","40/1308",1,{"$nulls":5},"5","210","98","156","71","149","79","0","0","0","0.6329",{"$nulls":31},"Unknown",-1,"AD/AR","Ellis-van Creveld syndrome; Weyers acrodental dysostosis","Cardiovascular; Craniofacial; Dental; Dermatologic; Musculoskeletal",null,"This gene encodes a protein that functions in bone formation and skeletal development. Mutations in this gene, as well as in a neighboring gene that lies in a head-to-head configuration, cause Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia that is also known as chondroectodermal dysplasia. Mutations in this gene also cause acrofacial dysostosis Weyers type, also referred to as Curry-Hall syndrome, a disease that combines limb and facial abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009].",null,"C0013903| C0457013","0/0","246,0","0","246","0/1","35,61","0.6354","96",null,"chr4:5708362:TGGGGATCCCGGGGTGGCTGCGCGCCGAGGGGGC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4225"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","EXO1","chr1:241853409","EXO1(K111N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch- containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:10608837, ECO:0000269|PubMed:11809771, ECO:0000269|PubMed:11842105, ECO:0000269|PubMed:12414623, ECO:0000269|PubMed:12704184, ECO:0000269|PubMed:14636568, ECO:0000269|PubMed:14676842, ECO:0000269|PubMed:15225546, ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:16143102, ECO:0000269|PubMed:9685493}.; ","level2",{"$nulls":3},"p.Lys111Asn","c.333A>T","MODERATE","111/846",4,{"$nulls":5},"4","251","296","172","194","232","265","0","0","0","0.234",{"$nulls":20},"2.232155","0.88","1.61;.;.;1.61;1.61;.;.","0.995174","-3.74;-3.33;-4.02;-3.74;-3.74;-3.33;-3.88","0.912;.;.;0.912;0.961;.;.","0.003;0.882;0.724;0.003;0.003;0.434;0.372","0.493;.;.;0.497;0.56;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMISMATCH_REPAIR",{"$nulls":3},"0/0","252,0","0","252","0/1","223,67","0.231","290",null,"chr1:241853409:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2062"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","EXO1","chr1:241853409","EXO1(K111N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch- containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:10608837, ECO:0000269|PubMed:11809771, ECO:0000269|PubMed:11842105, ECO:0000269|PubMed:12414623, ECO:0000269|PubMed:12704184, ECO:0000269|PubMed:14636568, ECO:0000269|PubMed:14676842, ECO:0000269|PubMed:15225546, ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:16143102, ECO:0000269|PubMed:9685493}.; ","level2",{"$nulls":3},"p.Lys111Asn","c.333A>T","MODERATE","111/846",4,{"$nulls":5},"4","251","294","172","199","234","256","0","0","0","0.3672",{"$nulls":20},"2.232155","0.88","1.61;.;.;1.61;1.61;.;.","0.995174","-3.74;-3.33;-4.02;-3.74;-3.74;-3.33;-3.88","0.912;.;.;0.912;0.961;.;.","0.003;0.882;0.724;0.003;0.003;0.434;0.372","0.493;.;.;0.497;0.56;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMISMATCH_REPAIR",{"$nulls":3},"0/0","240,0","0","240","0/1","161,103","0.3902","264",null,"chr1:241853409:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3518"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","EZH1","chr17:42713303","EZH1(H365fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Polycomb group (PcG) protein. Catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. Able to mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. Required for embryonic stem cell derivation and self-renewal, suggesting that it is involved in safeguarding embryonic stem cell identity. Compared to EZH2-containing complexes, it is less abundant in embryonic stem cells, has weak methyltransferase activity and plays a less critical role in forming H3K27me3, which is required for embryonic stem cell identity and proper differentiation. {ECO:0000269|PubMed:19026781}.; ","gedi",{"$nulls":3},"p.His365fs","c.1094_1109delACCACATAGTCAGTGC","HIGH","365/747",11,{"$nulls":5},"5","423","474","300","301","328","354","0","0","0","0.1328",{"$nulls":5},"(EZH1|ENSG00000108799|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"EZH1 is a component of a noncanonical Polycomb repressive complex-2 (PRC2) that mediates methylation of histone H3 (see MIM 602812) lys27 (H3K27) and functions in the maintenance of embryonic stem cell pluripotency and plasticity (Shen et al., 2008 [PubMed 19026780]).[supplied by OMIM, Mar 2009].  ",null,null,"0/0","435,0","0","435","0/1","387,53","0.1205","440",null,"chr17:42713303:AGCACTGACTATGTGGT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.113"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","F10","chr13:113149326","F10(R426C)",{"$nulls":6},255,"PASS","Missense","rs770671957",6.06e-05,"DISEASE: Factor X deficiency (FA10D) [MIM:227600]: A hemorrhagic disease with variable presentation. Affected individuals can manifest prolonged nasal and mucosal hemorrhage, menorrhagia, hematuria, and occasionally hemarthrosis. Some patients do not have clinical bleeding diathesis. {ECO:0000269|PubMed:10468877, ECO:0000269|PubMed:10739379, ECO:0000269|PubMed:10746568, ECO:0000269|PubMed:11248282, ECO:0000269|PubMed:11728527, ECO:0000269|PubMed:12574802, ECO:0000269|PubMed:12945883, ECO:0000269|PubMed:15075089, ECO:0000269|PubMed:15650540, ECO:0000269|PubMed:17393015, ECO:0000269|PubMed:19135706, ECO:0000269|PubMed:1973167, ECO:0000269|PubMed:1985698, ECO:0000269|PubMed:25313940, ECO:0000269|PubMed:26222694, ECO:0000269|PubMed:2790181, ECO:0000269|PubMed:7669671, ECO:0000269|PubMed:7860069, ECO:0000269|PubMed:8529633, ECO:0000269|PubMed:8845463, ECO:0000269|PubMed:8910490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.; ",{"$nulls":4},"p.Arg426Cys","c.1276C>T","MODERATE","426/488",8,1,{"$nulls":4},"4","1141","1135","880","862","952","958","0","0","0","0.1649",{"$nulls":20},"3.210871","-2.48","2.95","0.999986;1;1","-4.56","1.0","0.014","0.911",{"$nulls":3},"ExAC_SAS_AF",6.06e-05,"AR","Factor X deficiency","Hematologic",{"$nulls":3},"C0015519","0/0","1104,1","0.0009","1105","0/1","888,193","0.1785","1081",null,"chr13:113149326:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1729"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FAAH","chr1:46406278","FAAH(S289fs)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Degrades bioactive fatty acid amides like oleamide, the endogenous cannabinoid, anandamide and myristic amide to their corresponding acids, thereby serving to terminate the signaling functions of these molecules. Hydrolyzes polyunsaturated substrate anandamide preferentially as compared to monounsaturated substrates. {ECO:0000269|PubMed:17015445}.; ",{"$nulls":4},"p.Ser289fs","c.865_866dupAG","HIGH","289/579",7,{"$nulls":5},"5","716","713","542","536","609","665","0","0","0","0.1293",{"$nulls":5},"(FAAH|ENSG00000117480|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":6},"C1847831","0/0","664,0","0","664","0/1","573,86","0.1305","659",null,"chr1:46406278:G:GGA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1194"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FAM151A","chr1:54610487","FAM151A(D337H)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp337His","c.1009G>C","MODERATE","337/585",7,{"$nulls":5},"5","503","647","352","434","454","564","0","0","0","0.1011",{"$nulls":20},"0.907941","2.94","0.895","0.999996;1;0.999996","-0.6","0.454","0.097","0.238",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","500,0","0","500","0/1","555,69","0.1106","624",null,"chr1:54610487:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1175"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FAM151A","chr1:54610487","FAM151A(D337H)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp337His","c.1009G>C","MODERATE","337/585",7,{"$nulls":5},"5","503","631","352","429","455","563","0","0","0","0.151",{"$nulls":20},"0.907941","2.94","0.895","0.999996;1;0.999996","-0.6","0.454","0.097","0.238",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","493,0","0","493","0/1","509,104","0.1697","613",null,"chr1:54610487:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1632"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FAM192A","chr16:57167098","FAM192A(H159Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Promotes the association of the proteasome activator complex subunit PSME3 with the 20S proteasome and regulates its activity. Inhibits PSME3-mediated degradation of some proteasome substrates, probably by affecting their diffusion rate into the catalytic chamber of the proteasome. Also inhibits the interaction of PSME3 with COIL, inhibits accumulation of PSME3 in Cajal bodies and positively regulates the number of Cajal bodies in the nucleus. {ECO:0000269|PubMed:29934401}.; ",{"$nulls":4},"p.His159Gln","c.477T>G","MODERATE","159/254",5,{"$nulls":5},"4","330","424","240","283",null,null,"0","0",{"$nulls":22},"1.783657",null,null,"0.993211","-0.22;-0.22;-0.02;-0.22;-0.22;-0.22;-0.03;0.12","0.001;0.001;.;0.001;0.001;0.001;.;.","0.122;0.122;0.215;0.122;0.122;0.122;0.152;0.171","0.282;0.415;0.382;0.282;0.255;0.282;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","328,0","0","328","0/1","392,22","0.0531","414",null,"chr16:57167098:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.053"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FAM200B","chr4:15687085","FAM200B(E36D)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu36Asp","c.108G>T","MODERATE","36/657",2,{"$nulls":5},"5","80","58","68","50","60","43","0","0","0","0.3488",{"$nulls":20},"1.441738",".;2.57","-0.17","1",".;-0.49","0.003",".;0.026","0.05;0.053",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","76,0","0","76","0/1","36,20","0.3571","56",null,"chr4:15687085:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.38"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FAM200B","chr4:15687085","FAM200B(E36D)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu36Asp","c.108G>T","MODERATE","36/657",2,{"$nulls":5},"5","80","45","68","40","60","35","0","0","0","0.7714",{"$nulls":20},"1.441738",".;2.57","-0.17","1",".;-0.49","0.003",".;0.026","0.05;0.053",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","76,0","0","76","0/1","12,33","0.7333","45",null,"chr4:15687085:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.775"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FAM213A","chr10:80420471","FAM213A(S2P)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser2Pro","c.4T>C","MODERATE","2/229",1,{"$nulls":5},"5","291","370","237","287","230","308","0","0","0","0.1396",{"$nulls":20},"2.336392",null,null,"1;0.889795;0.889795;0.889795","-0.07;.;.;-0.07;-0.07","0.004","0.141;.;.;0.141;0.141","0.287;0.203;0.287;0.287;0.204",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","285,0","0","285","0/1","320,46","0.1257","366",null,"chr10:80420471:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1254"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FAM213A","chr10:80420471","FAM213A(S2P)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser2Pro","c.4T>C","MODERATE","2/229",1,{"$nulls":5},"5","291","241","237","193","230","201","0","0","0","0.2488",{"$nulls":20},"2.336392",null,null,"1;0.889795;0.889795;0.889795","-0.07;.;.;-0.07;-0.07","0.004","0.141;.;.;0.141;0.141","0.287;0.203;0.287;0.287;0.204",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","285,0","0","285","0/1","174,55","0.2402","229",null,"chr10:80420471:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.228"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FAM71A","chr1:212626161","FAM71A(D430fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Asp430fs","c.1290_1306delCAGGGCTCTCGGAAGGA","HIGH","430/594",1,{"$nulls":5},"5","389","152","300","118","290","117","0","0","0","0.265",{"$nulls":5},"(FAM71A|ENSG00000162771|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","394,0","0","394","0/1","115,39","0.2532","154",null,"chr1:212626161:AAAGGACAGGGCTCTCGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2797"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FASTK","chr7:151078002","FASTK(R306G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Phosphorylates the splicing regulator TIA1, thereby promoting the inclusion of FAS exon 6, which leads to an mRNA encoding a pro-apoptotic form of the receptor. {ECO:0000269|PubMed:17135269, ECO:0000269|PubMed:7544399}.; ","mitocarta",{"$nulls":3},"p.Arg306Gly","c.916C>G","MODERATE","306/549",5,{"$nulls":5},"5","518","531","388","367","445","466","0","0","0","0.1245",{"$nulls":20},"3.343753",".;0.9;0.9;0.9",".;.;0;.","0.685698;0.685698;0.685698;0.685698;1",".;-2.88;-2.87;-2.87",".;.;0.597;.",".;0.03;0.047;0.166","0.435;0.37;0.454;0.451",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","512,0","0","512","0/1","448,62","0.1216","510",null,"chr7:151078002:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1199"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FASTK","chr7:151078002","FASTK(R306G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Phosphorylates the splicing regulator TIA1, thereby promoting the inclusion of FAS exon 6, which leads to an mRNA encoding a pro-apoptotic form of the receptor. {ECO:0000269|PubMed:17135269, ECO:0000269|PubMed:7544399}.; ","mitocarta",{"$nulls":3},"p.Arg306Gly","c.916C>G","MODERATE","306/549",5,{"$nulls":5},"5","518","237","388","178","444","202","0","0","0","0.297",{"$nulls":20},"3.343753",".;0.9;0.9;0.9",".;.;0;.","0.685698;0.685698;0.685698;0.685698;1",".;-2.88;-2.87;-2.87",".;.;0.597;.",".;0.03;0.047;0.166","0.435;0.37;0.454;0.451",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","511,0","0","511","0/1","159,73","0.3147","232",null,"chr7:151078002:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.309"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FAT3","chr11:92765048","FAT3(S1385C)",null,null,"topological domain (Extracellular ), domain (Cadherin 13 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the interactions between neurites derived from specific subsets of neurons during development. {ECO:0000250}.; ",{"$nulls":4},"p.Ser1385Cys","c.4154C>G","MODERATE","1385/4557",5,{"$nulls":5},"5","370","560","254","373","323","475","0","0","0","0.1663",{"$nulls":20},"3.82118","0.02","2.225;.","0.999968","-3.36;-3.28",null,"0.003;0.002","0.867;0.864",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","371,0","0","371","0/1","454,97","0.176","551",null,"chr11:92765048:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1743"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FAT3","chr11:92765048","FAT3(S1385C)",null,null,"topological domain (Extracellular ), domain (Cadherin 13 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the interactions between neurites derived from specific subsets of neurons during development. {ECO:0000250}.; ",{"$nulls":4},"p.Ser1385Cys","c.4154C>G","MODERATE","1385/4557",5,{"$nulls":5},"5","370","276","254","190","321","232","0","0","0","0.1897",{"$nulls":20},"3.82118","0.02","2.225;.","0.999968","-3.36;-3.28",null,"0.003;0.002","0.867;0.864",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","369,0","0","369","0/1","198,59","0.2296","257",null,"chr11:92765048:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2316"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FBXO2","chr1:11650718","FBXO2(L47V)",null,null,"domain (F-box )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Involved in the endoplasmic reticulum-associated degradation pathway (ERAD) for misfolded lumenal proteins by recognizing and binding sugar chains on unfolded glycoproteins that are retrotranslocated into the cytosol and promoting their ubiquitination and subsequent degradation. Prevents formation of cytosolic aggregates of unfolded glycoproteins that have been retrotranslocated into the cytosol. Able to recognize and bind denatured glycoproteins, preferentially those of the high-mannose type (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu47Val","c.139C>G","MODERATE","47/296",2,{"$nulls":5},"5","209","168","156","125","164","115","0","0","0","0.2174",{"$nulls":20},"2.594619","1.78;.","0.74;.","0.984564","0.37;.","0.979;.","0.164;.","0.138;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","206,0","0","206","0/1","116,41","0.2611","157",null,"chr1:11650718:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.264"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FBXO2","chr1:11650718","FBXO2(L47V)",null,null,"domain (F-box )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Involved in the endoplasmic reticulum-associated degradation pathway (ERAD) for misfolded lumenal proteins by recognizing and binding sugar chains on unfolded glycoproteins that are retrotranslocated into the cytosol and promoting their ubiquitination and subsequent degradation. Prevents formation of cytosolic aggregates of unfolded glycoproteins that have been retrotranslocated into the cytosol. Able to recognize and bind denatured glycoproteins, preferentially those of the high-mannose type (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu47Val","c.139C>G","MODERATE","47/296",2,{"$nulls":5},"5","209","105","156","83","164","75","0","0","0","0.56",{"$nulls":20},"2.594619","1.78;.","0.74;.","0.984564","0.37;.","0.979;.","0.164;.","0.138;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","206,0","0","206","0/1","42,61","0.5922","103",null,"chr1:11650718:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5663"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FBXO31","chr16:87383561","FBXO31(P62S)",null,null,"compositionally biased region (Poly-Pro ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs1000666818",-1,"DISEASE: Mental retardation, autosomal recessive 45 (MRT45) [MIM:615979]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT45 manifestations include mild to moderate intellectual disability and dysmorphic features, including coarse facies, broad nasal bridge, fleshy nares, and thick, prominent lips. {ECO:0000269|PubMed:24623383}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of some SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. Specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. May act as a tumor suppressor. {ECO:0000269|PubMed:16357137, ECO:0000269|PubMed:19412162}.; ",{"$nulls":4},"p.Pro62Ser","c.184C>T","MODERATE","62/539",1,{"$nulls":5},"5","352","265","238","174","288","221","0","0","0","0.1674",{"$nulls":20},"2.17936","0.63;.","1.24;.","0.939513","-0.4;.","0.003;.","0.227;.","0.152;.",{"$nulls":3},"Unknown",-1,"AR","Mental retardation 45, autosomal recessive","Craniofacial; Neurologic",{"$nulls":3},"C4014864","0/0","346,0","0","346","0/1","214,39","0.1542","253",null,"chr16:87383561:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1552"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FBXO31","chr16:87383561","FBXO31(P62S)",null,null,"compositionally biased region (Poly-Pro ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs1000666818",-1,"DISEASE: Mental retardation, autosomal recessive 45 (MRT45) [MIM:615979]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT45 manifestations include mild to moderate intellectual disability and dysmorphic features, including coarse facies, broad nasal bridge, fleshy nares, and thick, prominent lips. {ECO:0000269|PubMed:24623383}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Component of some SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. Specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. May act as a tumor suppressor. {ECO:0000269|PubMed:16357137, ECO:0000269|PubMed:19412162}.; ",{"$nulls":4},"p.Pro62Ser","c.184C>T","MODERATE","62/539",1,{"$nulls":5},"5","352","184","238","127","290","156","0","0","0","0.3782",{"$nulls":20},"2.17936","0.63;.","1.24;.","0.939513","-0.4;.","0.003;.","0.227;.","0.152;.",{"$nulls":3},"Unknown",-1,"AR","Mental retardation 45, autosomal recessive","Craniofacial; Neurologic",{"$nulls":3},"C4014864","0/0","346,0","0","346","0/1","113,70","0.3825","183",null,"chr16:87383561:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3937"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FBXW7","chr4:152328238","FBXW7(T463S)",null,null,"repeat (WD 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes and binds phosphorylated sites/phosphodegrons within target proteins and thereafter bring them to the SCF complex for ubiquitination (PubMed:22748924, PubMed:17434132, PubMed:26976582, PubMed:28727686). Identified substrates include cyclin-E (CCNE1 or CCNE2), DISC1, JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NOTCH2, MCL1, and probably PSEN1 (PubMed:11565034, PubMed:12354302, PubMed:11585921, PubMed:15103331, PubMed:14739463, PubMed:17558397, PubMed:17873522, PubMed:22608923, PubMed:22748924, PubMed:29149593, PubMed:25775507, PubMed:28007894, PubMed:26976582, PubMed:28727686). Acts as a negative regulator of JNK signaling by binding to phosphorylated JUN and promoting its ubiquitination and subsequent degradation (PubMed:14739463). SCF(FBXW7) complex mediates the ubiquitination and subsequent degradation of NFE2L1 (By similarity). Involved in bone homeostasis and negative regulation of osteoclast differentiation (PubMed:29149593). {ECO:0000250|UniProtKB:Q8VBV4, ECO:0000269|PubMed:11565034, ECO:0000269|PubMed:11585921, ECO:0000269|PubMed:14739463, ECO:0000269|PubMed:15103331, ECO:0000269|PubMed:17434132, ECO:0000269|PubMed:17558397, ECO:0000269|PubMed:17873522, ECO:0000269|PubMed:22608923, ECO:0000269|PubMed:22748924, ECO:0000269|PubMed:25775507, ECO:0000269|PubMed:26976582, ECO:0000269|PubMed:28007894, ECO:0000269|PubMed:28727686, ECO:0000269|PubMed:29149593, ECO:0000305|PubMed:12354302}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Everolimus\" , \"Paclitaxel\" , \"Sirolimus\" , \"Sorafenib\" , \"Temsirolimus\" , \"Vinblastine\" , \"Vincristine\" , \"Vinorelbine\" , \"Vorinostat\"]","[ \"Everolimus\" , \"Paclitaxel\" , \"Sirolimus\" , \"Sorafenib\" , \"Temsirolimus\" , \"Vinblastine\" , \"Vincristine\" , \"Vinorelbine\" , \"Vorinostat\"]","[ \"Everolimus\" , \"Paclitaxel\" , \"Sirolimus\" , \"Sorafenib\" , \"Temsirolimus\" , \"Vinblastine\" , \"Vincristine\" , \"Vinorelbine\" , \"Vorinostat\"]","p.Thr463Ser","c.1388C>G","MODERATE","463/707",9,1,{"$nulls":4},"5","472","491","368","376","368","402","0","0","0","0.3358",{"$nulls":20},"3.925672","1.02;1.02;1.02;.;1.02;1.02","0.18;.;0.18;.;.;0.18","1",".;-3.91;-3.97;.;-3.91;.","1.0",".;0.005;0.066;.;0.003;.","0.629;0.622;0.624;.;0.616;0.626",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC,vCIN",{"$nulls":3},"0/0","457,0","0","457","0/1","326,136","0.2944","462",null,"chr4:152328238:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3005"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","FBXW7","chr4:152328238","FBXW7(T463S)",null,null,"repeat (WD 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes and binds phosphorylated sites/phosphodegrons within target proteins and thereafter bring them to the SCF complex for ubiquitination (PubMed:22748924, PubMed:17434132, PubMed:26976582, PubMed:28727686). Identified substrates include cyclin-E (CCNE1 or CCNE2), DISC1, JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NOTCH2, MCL1, and probably PSEN1 (PubMed:11565034, PubMed:12354302, PubMed:11585921, PubMed:15103331, PubMed:14739463, PubMed:17558397, PubMed:17873522, PubMed:22608923, PubMed:22748924, PubMed:29149593, PubMed:25775507, PubMed:28007894, PubMed:26976582, PubMed:28727686). Acts as a negative regulator of JNK signaling by binding to phosphorylated JUN and promoting its ubiquitination and subsequent degradation (PubMed:14739463). SCF(FBXW7) complex mediates the ubiquitination and subsequent degradation of NFE2L1 (By similarity). Involved in bone homeostasis and negative regulation of osteoclast differentiation (PubMed:29149593). {ECO:0000250|UniProtKB:Q8VBV4, ECO:0000269|PubMed:11565034, ECO:0000269|PubMed:11585921, ECO:0000269|PubMed:14739463, ECO:0000269|PubMed:15103331, ECO:0000269|PubMed:17434132, ECO:0000269|PubMed:17558397, ECO:0000269|PubMed:17873522, ECO:0000269|PubMed:22608923, ECO:0000269|PubMed:22748924, ECO:0000269|PubMed:25775507, ECO:0000269|PubMed:26976582, ECO:0000269|PubMed:28007894, ECO:0000269|PubMed:28727686, ECO:0000269|PubMed:29149593, ECO:0000305|PubMed:12354302}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Everolimus\" , \"Paclitaxel\" , \"Sirolimus\" , \"Sorafenib\" , \"Temsirolimus\" , \"Vinblastine\" , \"Vincristine\" , \"Vinorelbine\" , \"Vorinostat\"]","[ \"Everolimus\" , \"Paclitaxel\" , \"Sirolimus\" , \"Sorafenib\" , \"Temsirolimus\" , \"Vinblastine\" , \"Vincristine\" , \"Vinorelbine\" , \"Vorinostat\"]","[ \"Everolimus\" , \"Paclitaxel\" , \"Sirolimus\" , \"Sorafenib\" , \"Temsirolimus\" , \"Vinblastine\" , \"Vincristine\" , \"Vinorelbine\" , \"Vorinostat\"]","p.Thr463Ser","c.1388C>G","MODERATE","463/707",9,1,{"$nulls":4},"5","472","230","368","184","370","191","0","0","0","0.6387",{"$nulls":20},"3.925672","1.02;1.02;1.02;.;1.02;1.02","0.18;.;0.18;.;.;0.18","1",".;-3.91;-3.97;.;-3.91;.","1.0",".;0.005;0.066;.;0.003;.","0.629;0.622;0.624;.;0.616;0.626",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC,vCIN",{"$nulls":3},"0/0","468,0","0","468","0/1","91,135","0.5973","226",null,"chr4:152328238:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5924"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","FER1L6","chr8:123975236","FER1L6(S205C)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser205Cys","c.613A>T","MODERATE","205/1857",8,{"$nulls":5},"4","334","444","243","325",null,null,"0","0",{"$nulls":22},"2.933663","-1.43","1.79","0.999993","-3.34","0.996","0.003","0.574",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","324,1","0.0031","325","0/1","368,55","0.13","423",null,"chr8:123975236:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1262"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GABRP","chr5:170809750","GABRP(D339H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. In the uterus, the function of the receptor appears to be related to tissue contractility. The binding of this pI subunit with other GABA(A) receptor subunits alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone.; ",{"$nulls":4},"p.Asp339His","c.1015G>C","MODERATE","339/440",9,{"$nulls":5},"5","391","400","266","271","371","367","0","0","0","0.3488",{"$nulls":20},"3.634323","-2.0;-2.0;-1.43","0;0;.","0.981615;0.999345;0.981615;1","-0.54;-0.54;-0.53","0.927;0.927;.","0.1;0.1;0.016","0.471;0.467;0.438",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","391,0","0","391","0/1","247,150","0.3778","397",null,"chr5:170809750:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3653"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","GABRP","chr5:170809750","GABRP(D339H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. In the uterus, the function of the receptor appears to be related to tissue contractility. The binding of this pI subunit with other GABA(A) receptor subunits alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone.; ",{"$nulls":4},"p.Asp339His","c.1015G>C","MODERATE","339/440",9,{"$nulls":5},"5","391","272","266","192","367","236","0","0","0","0.7415",{"$nulls":20},"3.634323","-2.0;-2.0;-1.43","0;0;.","0.981615;0.999345;0.981615;1","-0.54;-0.54;-0.53","0.927;0.927;.","0.1;0.1;0.016","0.471;0.467;0.438",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","386,0","0","386","0/1","66,204","0.7556","270",null,"chr5:170809750:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7552"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GART","chr21:33505565","GART(W907C)",null,null,"region of interest (GART ), splice variant (In isoform Short. ), turn ",{"$nulls":3},255,"PASS","Missense",null,-1,null,null,"gedi",{"$nulls":3},"p.Trp907Cys","c.2721G>C","MODERATE","907/1010",20,{"$nulls":5},"5","219","262","183","219","169","203","0","0","0","0.1133",{"$nulls":20},"4.414704","-1.04","2.91","1","-12.32","1.0","0.0","0.952;0.874;0.953",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","222,0","0","222","0/1","223,32","0.1255","255",null,"chr21:33505565:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1324"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","GART","chr21:33505565","GART(W907C)",null,null,"region of interest (GART ), splice variant (In isoform Short. ), turn ",{"$nulls":3},255,"PASS","Missense",null,-1,null,null,"gedi",{"$nulls":3},"p.Trp907Cys","c.2721G>C","MODERATE","907/1010",20,{"$nulls":5},"5","219","116","183","98","169","90","0","0","0","0.3111",{"$nulls":20},"4.414704","-1.04","2.91","1","-12.32","1.0","0.0","0.952;0.874;0.953",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","222,0","0","222","0/1","79,31","0.2818","110",null,"chr21:33505565:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2959"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GFAP","chr17:44911337","GFAP(M342I)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Alexander disease (ALXDRD) [MIM:203450]: A rare disorder of the central nervous system. The most common form affects infants and young children, and is characterized by progressive failure of central myelination, usually leading to death within the first decade. Infants with Alexander disease develop a leukodystrophy with macrocephaly, seizures, and psychomotor retardation. Patients with juvenile or adult forms typically experience ataxia, bulbar signs and spasticity, and a more slowly progressive course. Histologically, Alexander disease is characterized by Rosenthal fibers, homogeneous eosinophilic inclusions in astrocytes. {ECO:0000269|PubMed:11138011, ECO:0000269|PubMed:11567214, ECO:0000269|PubMed:11595337, ECO:0000269|PubMed:12034785, ECO:0000269|PubMed:12034796, ECO:0000269|PubMed:12581808, ECO:0000269|PubMed:12944715, ECO:0000269|PubMed:12975300, ECO:0000269|PubMed:15030911, ECO:0000269|PubMed:15732097, ECO:0000269|PubMed:17043438, ECO:0000269|PubMed:17805552, ECO:0000269|PubMed:17894839, ECO:0000269|PubMed:17934883, ECO:0000269|PubMed:17960815, ECO:0000269|PubMed:18004641, ECO:0000269|PubMed:18079314, ECO:0000269|PubMed:19412928, ECO:0000269|PubMed:20359319, ECO:0000269|PubMed:21917775, ECO:0000269|PubMed:23364391, ECO:0000269|PubMed:23743246, ECO:0000269|PubMed:24742911}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: GFAP, a class-III intermediate filament, is a cell- specific marker that, during the development of the central nervous system, distinguishes astrocytes from other glial cells.; ",{"$nulls":4},"p.Met342Ile","c.1026G>T","MODERATE","342/438",6,{"$nulls":5},"5","274","250","213","181","220","188","0","0","0","0.1117",{"$nulls":20},"4.269443",".;.;-2.58;.;-2.58;.",".;1.925;.;.;1.925;1.925","1",".;.;-3.67;.;-3.67;.",".;0.988;.;.;.;.",".;.;0.025;.;0.03;.",".;.;0.909;.;0.911;.",{"$nulls":3},"Unknown",-1,"AD","Alexander disease","Neurologic",{"$nulls":3},"C0270726","0/0","266,0","0","266","0/1","217,22","0.0921","239",null,"chr17:44911337:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0939"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GGT5","chr22:24225013","GGT5(E534K)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs776231440",8.246e-06,null,"FUNCTION: Cleaves the gamma-glutamyl peptide bond of glutathione conjugates, but maybe not glutathione itself. Converts leukotriene C4 (LTC4) to leukotriene D4 (LTD4).; ",{"$nulls":4},"p.Glu534Lys","c.1600G>A","MODERATE","534/587",11,{"$nulls":5},"5","250","293","209","232","180","226","0","0","0","0.146",{"$nulls":20},"3.19589","1.81",".;3.525;.","0.999995","-3.69","1.0;1.0;.","0.005","0.602;0.544;0.543",{"$nulls":3},"ExAC_AF",8.246e-06,{"$nulls":7},"0/0","247,0","0","247","0/1","229,42","0.155","271",null,"chr22:24225013:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1509"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","GGT5","chr22:24225013","GGT5(E534K)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs776231440",8.246e-06,null,"FUNCTION: Cleaves the gamma-glutamyl peptide bond of glutathione conjugates, but maybe not glutathione itself. Converts leukotriene C4 (LTC4) to leukotriene D4 (LTD4).; ",{"$nulls":4},"p.Glu534Lys","c.1600G>A","MODERATE","534/587",11,{"$nulls":5},"5","250","224","209","193","180","170","0","0","0","0.2353",{"$nulls":20},"3.19589","1.81",".;3.525;.","0.999995","-3.69","1.0;1.0;.","0.005","0.602;0.544;0.543",{"$nulls":3},"ExAC_AF",8.246e-06,{"$nulls":7},"0/0","245,0","0","245","0/1","174,47","0.2127","221",null,"chr22:24225013:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2176"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GLTSCR1","chr19:47680104","GLTSCR1(A312P)",{"$nulls":6},255,"PASS","Missense","rs942313852",-1,{"$nulls":6},"p.Ala312Pro","c.934G>C","MODERATE","312/1560",6,{"$nulls":5},"5","270","268","230","231","190","227","0.0038","0.0038","0","0.2555",{"$nulls":20},"1.621567","1.43;.",null,"1","-1.62;.","0.003;.","0.006;.","0.305;0.318",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","257,1","0.0039","258","0/1","195,67","0.2557","262",null,"chr19:47680104:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2597"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","GLTSCR1","chr19:47680104","GLTSCR1(A312P)",{"$nulls":6},255,"PASS","Missense","rs942313852",-1,{"$nulls":6},"p.Ala312Pro","c.934G>C","MODERATE","312/1560",6,{"$nulls":5},"5","270","163","230","143","190","131","0.0038","0.0038","0","0.771",{"$nulls":20},"1.621567","1.43;.",null,"1","-1.62;.","0.003;.","0.006;.","0.305;0.318",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","257,1","0.0039","258","0/1","37,116","0.7582","153",null,"chr19:47680104:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7552"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GRK1","chr13:113733037","GRK1(R450C)",null,null,"domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense","rs779956968",0.0001274,"DISEASE: Night blindness, congenital stationary, Oguchi type 2 (CSNBO2) [MIM:613411]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. Congenital stationary night blindness Oguchi type is associated with fundus discoloration and abnormally slow dark adaptation. {ECO:0000269|PubMed:17070587, ECO:0000269|PubMed:9020843}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Retina-specific kinase involved in the signal turnoff via phosphorylation of rhodopsin (RHO), the G protein- coupled receptor that initiates the phototransduction cascade. This rapid desensitization is essential for scotopic vision and permits rapid adaptation to changes in illumination. {ECO:0000269|PubMed:15946941}.; ",{"$nulls":4},"p.Arg450Cys","c.1348C>T","MODERATE","450/563",6,{"$nulls":5},"5","1048","1103","724","732","966","1009","0","0","0","0.2944",{"$nulls":20},"2.610808","1.81",null,"0.999526","-5.69","1.0",null,"0.379",{"$nulls":3},"ExAC_SAS_AF",0.0001274,"AR","Oguchi disease 2","Ophthalmologic",{"$nulls":3},"C3150678","0/0","1021,0","0","1021","0/1","714,309","0.3021","1023",null,"chr13:113733037:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2869"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","GRK1","chr13:113733037","GRK1(R450C)",null,null,"domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense","rs779956968",0.0001274,"DISEASE: Night blindness, congenital stationary, Oguchi type 2 (CSNBO2) [MIM:613411]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. Congenital stationary night blindness Oguchi type is associated with fundus discoloration and abnormally slow dark adaptation. {ECO:0000269|PubMed:17070587, ECO:0000269|PubMed:9020843}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Retina-specific kinase involved in the signal turnoff via phosphorylation of rhodopsin (RHO), the G protein- coupled receptor that initiates the phototransduction cascade. This rapid desensitization is essential for scotopic vision and permits rapid adaptation to changes in illumination. {ECO:0000269|PubMed:15946941}.; ",{"$nulls":4},"p.Arg450Cys","c.1348C>T","MODERATE","450/563",6,{"$nulls":5},"5","1048","986","724","689","969","889","0","0","0","0.3307",{"$nulls":20},"2.610808","1.81",null,"0.999526","-5.69","1.0",null,"0.379",{"$nulls":3},"ExAC_SAS_AF",0.0001274,"AR","Oguchi disease 2","Ophthalmologic",{"$nulls":3},"C3150678","0/0","1019,0","0","1019","0/1","630,306","0.3269","936",null,"chr13:113733037:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3353"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GSDMD","chr8:143559378","GSDMD(E63Q)",null,null,"turn ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Gasdermin-D, N-terminal: Promotes pyroptosis in response to microbial infection and danger signals. Produced by the cleavage of gasdermin-D by inflammatory caspases CASP1 or CASP4 in response to canonical, as well as non-canonical (such as cytosolic LPS) inflammasome activators (PubMed:26375003, PubMed:26375259, PubMed:27418190). After cleavage, moves to the plasma membrane where it strongly binds to inner leaflet lipids, including monophosphorylated phosphatidylinositols, such as phosphatidylinositol 4-phosphate, bisphosphorylated phosphatidylinositols, such as phosphatidylinositol (4,5)- bisphosphate, as well as phosphatidylinositol (3,4,5)- bisphosphate, and more weakly to phosphatidic acid and phosphatidylserine (PubMed:27281216). Homooligomerizes within the membrane and forms pores of 10 - 15 nanometers (nm) of inner diameter, possibly allowing the release of mature IL1B and triggering pyroptosis (PubMed:27418190, PubMed:27281216). Exhibits bactericidal activity. Gasdermin-D, N-terminal released from pyroptotic cells into the extracellular milieu rapidly binds to and kills both Gram-negative and Gram-positive bacteria, without harming neighboring mammalian cells, as it does not disrupt the plasma membrane from the outside due to lipid-binding specificity (PubMed:27281216). Under cell culture conditions, also active against intracellular bacteria, such as Listeria monocytogenes (By similarity). Strongly binds to bacterial and mitochondrial lipids, including cardiolipin. Does not bind to unphosphorylated phosphatidylinositol, phosphatidylethanolamine nor phosphatidylcholine (PubMed:27281216). {ECO:0000250|UniProtKB:Q9D8T2, ECO:0000269|PubMed:26375003, ECO:0000269|PubMed:26375259, ECO:0000269|PubMed:27281216, ECO:0000269|PubMed:27418190}.; ",{"$nulls":4},"p.Glu63Gln","c.187G>C","MODERATE","63/532",3,1,{"$nulls":4},"5","546","582","445","461","454","501","0","0","0","0.1317",{"$nulls":20},"3.357577","1.31","2.56;.;.;.;2.56;.;.;.","0.635288","-1.95;-2.71;-1.79;-1.95;-1.95;-1.52;-2.05;-1.82","0.995;.;.;0.994;0.995;.;.;.","0.541;0.0;0.383;0.405;0.541;0.417;0.269;0.413","0.478;.;.;0.479;0.478;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","535,0","0","535","0/1","490,73","0.1297","563",null,"chr8:143559378:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.128"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","GYS1","chr19:48982754","GYS1(R303*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1269675538",-1,"DISEASE: Muscle glycogen storage disease 0 (GSD0b) [MIM:611556]: Metabolic disorder characterized by fasting hypoglycemia presenting in infancy or early childhood. The role of muscle glycogen is to provide critical energy during bursts of activity and sustained muscle work. {ECO:0000269|PubMed:17928598}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan.; ",{"$nulls":4},"p.Arg303*","c.907C>T","HIGH","303/737",6,{"$nulls":5},"5","440","435","371","351","283","305","0","0","0","0.3803",{"$nulls":5},"(GYS1|ENSG00000104812|1|1.00)","(GYS1|ENSG00000104812|1|1.00)",{"$nulls":13},"8.279263",null,null,"1",{"$nulls":3},"0.952;0.947",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease, type 0, muscle","Biochemical; Cardiovascular; Musculoskeletal; Neurologic",{"$nulls":3},"C1969054","0/0","430,0","0","430","0/1","285,132","0.3165","417",null,"chr19:48982754:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3248"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","GYS1","chr19:48982754","GYS1(R303*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1269675538",-1,"DISEASE: Muscle glycogen storage disease 0 (GSD0b) [MIM:611556]: Metabolic disorder characterized by fasting hypoglycemia presenting in infancy or early childhood. The role of muscle glycogen is to provide critical energy during bursts of activity and sustained muscle work. {ECO:0000269|PubMed:17928598}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan.; ",{"$nulls":4},"p.Arg303*","c.907C>T","HIGH","303/737",6,{"$nulls":5},"5","440","258","371","203","283","197","0","0","0","0.7259",{"$nulls":5},"(GYS1|ENSG00000104812|1|1.00)","(GYS1|ENSG00000104812|1|1.00)",{"$nulls":13},"8.279263",null,null,"1",{"$nulls":3},"0.952;0.947",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease, type 0, muscle","Biochemical; Cardiovascular; Musculoskeletal; Neurologic",{"$nulls":3},"C1969054","0/0","430,0","0","430","0/1","82,166","0.6694","248",null,"chr19:48982754:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6749"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","HBS1L","chr6:134997503","HBS1L(Sequence Feature)",{"$nulls":3},"modified-residue:phosphothreonine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,{"$nulls":7},"c.693C>T","MODERATE",null,6,{"$nulls":5},"4","584","1235","413","892","503","1042","0","0","0","0.0672",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","551,0","0","551","0/1","1097,79","0.0672","1176",null,"chr6:134997503:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0684"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","HECTD4","chr12:112314526","HECTD4(V239A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. {ECO:0000250}.; ",{"$nulls":4},"p.Val239Ala","c.716T>C","MODERATE","239/4416",3,{"$nulls":5},"5","306","346","214","216","293","325","0","0","0","0.3354",{"$nulls":20},"3.2271","-2.88;.",null,"0.709099;0.709099;1","-1.22;.",null,"0.001;.","0.725;0.703",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","305,0","0","305","0/1","224,115","0.3392","339",null,"chr12:112314526:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3194"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","HECTD4","chr12:112314526","HECTD4(V239A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. {ECO:0000250}.; ",{"$nulls":4},"p.Val239Ala","c.716T>C","MODERATE","239/4416",3,{"$nulls":5},"5","306","171","214","118","293","152","0","0","0","0.6776",{"$nulls":20},"3.2271","-2.88;.",null,"0.709099;0.709099;1","-1.22;.",null,"0.001;.","0.725;0.703",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","301,0","0","301","0/1","49,117","0.7048","166",null,"chr12:112314526:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.678"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","HES6","chr2:238239663","HES6(E56Q)",null,null,"domain (bHLH )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Does not bind DNA itself but suppresses both HES1- mediated N box-dependent transcriptional repression and binding of HES1 to E box sequences. Also suppresses HES1-mediated inhibition of the heterodimer formed by ASCL1/MASH1 and TCF3/E47, allowing ASCL1 and TCF3 to up-regulate transcription in its presence. Promotes cell differentiation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu56Gln","c.166G>C","MODERATE","56/224",2,{"$nulls":5},"4",null,null,"74","63","61","47",null,null,"0","0.4894",{"$nulls":20},"3.357732","-4.41;-4.41;-4.59;-4.41","1.02","0.552084;0.552084;0.552084;1;1;0.995696","-1.45;-1.49;0.74;-1.76","0.049;0.997;0.001;.","0.139;0.03;0.89;0.219","0.145;0.085;0.129;0.118",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","85,0","0","85","0/1","45,30","0.4","75",null,"chr2:238239663:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.381"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","HES6","chr2:238239663","HES6(E56Q)",null,null,"domain (bHLH )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Does not bind DNA itself but suppresses both HES1- mediated N box-dependent transcriptional repression and binding of HES1 to E box sequences. Also suppresses HES1-mediated inhibition of the heterodimer formed by ASCL1/MASH1 and TCF3/E47, allowing ASCL1 and TCF3 to up-regulate transcription in its presence. Promotes cell differentiation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu56Gln","c.166G>C","MODERATE","56/224",2,{"$nulls":5},"5","85","41","74","37","61","28","0","0","0","0.3571",{"$nulls":20},"3.357732","-4.41;-4.41;-4.59;-4.41","1.02","0.552084;0.552084;0.552084;1;1;0.995696","-1.45;-1.49;0.74;-1.76","0.049;0.997;0.001;.","0.139;0.03;0.89;0.219","0.145;0.085;0.129;0.118",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","84,0","0","84","0/1","30,10","0.25","40",null,"chr2:238239663:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2703"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","HIGD2B","chr15:72676205","HIGD2B(A57V)",null,null,"transmembrane region (Helical ), domain (HIG1 )",{"$nulls":3},255,"PASS","Missense","rs774583212",4.405E-5,{"$nulls":6},"p.Ala57Val","c.170C>T","MODERATE","57/106",3,1,{"$nulls":4},"4","492","591","370","442","433","526","0","0","0","0.1293",{"$nulls":20},"0.522778",null,null,"0.998967","-1.46",null,"0.611","0.162",{"$nulls":3},"ExAC_NFE_AF",4.405E-5,{"$nulls":7},"0/0","485,0","0","485","0/1","492,82","0.1429","574",null,"chr15:72676205:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1425"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","HIP1","chr7:75557671","HIP1(D522Y)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving HIP1 is found in a form of chronic myelomonocytic leukemia (CMML). Translocation t(5;7)(q33;q11.2) with PDGFRB (PubMed:9616134). The chimeric HIP1- PDGFRB transcript results from an in-frame fusion of the two genes (PubMed:9616134). The reciprocal PDGFRB-HIP1 transcript is not expressed (PubMed:9616134). {ECO:0000269|PubMed:9616134}.; ","FUNCTION: Plays a role in clathrin-mediated endocytosis and trafficking (PubMed:11532990, PubMed:11577110, PubMed:11889126). Involved in regulating AMPA receptor trafficking in the central nervous system in an NMDA-dependent manner (By similarity). Regulates presynaptic nerve terminal activity (By similarity). Enhances androgen receptor (AR)-mediated transcription (PubMed:16027218). May act as a proapoptotic protein that induces cell death by acting through the intrinsic apoptosis pathway (PubMed:11007801). Binds 3-phosphoinositides (via ENTH domain) (PubMed:14732715). May act through the ENTH domain to promote cell survival by stabilizing receptor tyrosine kinases following ligand-induced endocytosis (PubMed:14732715). May play a functional role in the cell filament networks (PubMed:18790740). May be required for differentiation, proliferation, and/or survival of somatic and germline progenitors (PubMed:11007801, PubMed:12163454). {ECO:0000250|UniProtKB:Q8VD75, ECO:0000269|PubMed:11007801, ECO:0000269|PubMed:11532990, ECO:0000269|PubMed:11577110, ECO:0000269|PubMed:11889126, ECO:0000269|PubMed:12163454, ECO:0000269|PubMed:14732715, ECO:0000269|PubMed:16027218, ECO:0000269|PubMed:18790740, ECO:0000269|PubMed:9147654}.; ","level2",{"$nulls":3},"p.Asp522Tyr","c.1564G>T","MODERATE","522/1037",16,{"$nulls":5},"5","226","210","185","168","172","160","0","0","0","0.1562",{"$nulls":20},"2.859774","2.55;2.34;.","1.7;1.7;.","0.620629","-2.78;-2.73;.","0.707;.;.","0.023;0.022;.","0.428;0.396;0.421",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","220,0","0","220","0/1","174,25","0.1256","199",null,"chr7:75557671:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1369"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","HR","chr8:22127614","HR(W276C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Alopecia universalis congenita (ALUNC) [MIM:203655]: A rare disorder characterized by loss of hair from the entire body. No hair are present in hair follicles on skin biopsy. {ECO:0000269|PubMed:12406339, ECO:0000269|PubMed:24334705, ECO:0000269|PubMed:9445480, ECO:0000269|PubMed:9736769}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Atrichia with papular lesions (APL) [MIM:209500]: An autosomal recessive disease characterized by papillary lesions over most of the body and almost complete absence of hair. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypotrichosis 4 (HYPT4) [MIM:146550]: An autosomal dominant condition characterized by reduced amount of hair, alopecia, little or no eyebrows, eyelashes or body hair, and coarse, wiry, twisted hair in early childhood. {ECO:0000269|PubMed:19122663, ECO:0000269|PubMed:24961381}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Histone demethylase that specifically demethylates both mono- and dimethylated 'Lys-9' of histone H3. May act as a transcription regulator controlling hair biology (via targeting of collagens), neural activity, and cell cycle. {ECO:0000269|PubMed:24334705}.; ",{"$nulls":4},"p.Trp276Cys","c.828G>C","MODERATE","276/1189",3,{"$nulls":5},"5","288","252","229","187","229","213","0","0","0","0.1925",{"$nulls":20},"1.574573","-0.53;-0.54","0.69","1","0.79;0.74","0.0;0.001","0.0","0.177;0.246",{"$nulls":3},"Unknown",-1,"AD/AR","Hypotrichosis 4; Atrichia with papular lesions; Alopecia universalis congenita","Dermatologic",{"$nulls":3},"C1859592| C2750815| C1859877","0/0","283,0","0","283","0/1","200,49","0.1968","249",null,"chr8:22127614:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1604"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","IFI44L","chr1:78628064","IFI44L(T50I)",null,null,"domain (TLDc )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Exhibits a low antiviral activity against hepatitis C virus. {ECO:0000269|PubMed:21478870}.; ",{"$nulls":4},"p.Thr50Ile","c.149C>T","MODERATE","50/452",2,{"$nulls":5},"5","345","544","253","385","318","483","0","0","0","0.0642",{"$nulls":20},"0.686448","1.03;2.49;1.98",".;1.63;.","1;0.991672","-4.9;-4.69;-4.78",".;0.93;.","0.08;0.116;0.059",".;0.209;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","340,0","0","340","0/1","495,37","0.0695","532",null,"chr1:78628064:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0675"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","IFT20","chr17:28332188","IFT20(P12A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Part of intraflagellar transport (IFT) particles involved in ciliary process assembly. May play a role in the trafficking of ciliary membrane proteins from the Golgi complex to the cilium. Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment. {ECO:0000269|PubMed:16775004}.; ",{"$nulls":4},"p.Pro12Ala","c.34C>G","MODERATE","12/158",2,{"$nulls":5},"4","549","590","363","390","507","530","0","0","0","0.1302",{"$nulls":20},"2.054153",null,null,"1;1;1;1;0.993769;0.993769;0.993769",null,"0.058;.;.;.",null,"0.239;0.255;0.262;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","538,1","0.0019","539","0/1","479,70","0.1275","549",null,"chr17:28332188:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1308"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","IGSF22","chr11:18721955","IGSF22(V66I)",{"$nulls":6},255,"PASS","Missense","rs1233745017",-1,{"$nulls":6},"p.Val66Ile","c.196G>A","MODERATE","66/1326",3,{"$nulls":5},"5","635","696","466","489","537","586","0","0","0","0.1143",{"$nulls":20},"0.61936","0.68",null,"0.999999","-0.68",null,"0.321","0.14",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","624,0","0","624","0/1","583,77","0.1167","660",null,"chr11:18721955:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1247"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","IMPG2","chr3:101276688","IMPG2(V187I)",null,null,"topological domain (Extracellular ), sequence variant (In RP56. ), sequence variant (In RP56. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Retinitis pigmentosa 56 (RP56) [MIM:613581]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:20673862}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Macular dystrophy, vitelliform, 5 (VMD5) [MIM:616152]: A form of macular dystrophy, a retinal disease in which various forms of deposits, pigmentary changes, and atrophic lesions are observed in the macula lutea. Vitelliform macular dystrophies are characterized by yellow, lipofuscin-containing deposits, usually localized at the center of the macula. VMD5 features include late- onset moderate visual impairment and preservation of retinal pigment epithelium reflectivity. {ECO:0000269|PubMed:20673862, ECO:0000269|PubMed:25085631}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Chondroitin sulfate- and hyaluronan-binding proteoglycan involved in the organization of interphotoreceptor matrix; may participate in the maturation and maintenance of the light- sensitive photoreceptor outer segment. Binds heparin. {ECO:0000269|PubMed:10702256}.; ",{"$nulls":4},"p.Val187Ile","c.559G>A","MODERATE","187/1241",5,{"$nulls":5},"5","55","34","44","24","45","27","0","0","0","0.1852",{"$nulls":20},"0.794444","1.97","0.955","1","-0.34","0.001","0.484","0.065",{"$nulls":3},"Unknown",-1,"AR","Retinitis pigmentosa 56","Ophthalmologic",{"$nulls":3},"C3150819| C4015343","0/0","54,0","0","54","0/1","29,5","0.1471","34",null,"chr3:101276688:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.125"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ING5","chr2:241704699","ING5(M30I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the HBO1 complex which has a histone H4- specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo. Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Through chromatin acetylation it may regulate DNA replication and may function as a transcriptional coactivator (PubMed:12750254, PubMed:16387653). Inhibits cell growth, induces a delay in S-phase progression and enhances Fas-induced apoptosis in an INCA1-dependent manner (PubMed:21750715). {ECO:0000269|PubMed:12750254, ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:21750715}.; ",{"$nulls":4},"p.Met30Ile","c.90G>C","MODERATE","30/254",3,{"$nulls":5},"5","394","482","268","312","364","440","0","0","0","0.0955",{"$nulls":20},"3.068842",null,".;1.595;1.595","1",".;-3.58;-3.52",".;0.999;.",".;0.107;0.053",".;0.843;0.838",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","387,0","0","387","0/1","409,43","0.0951","452",null,"chr2:241704699:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0833"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ING5","chr2:241704699","ING5(M30I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the HBO1 complex which has a histone H4- specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo. Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Through chromatin acetylation it may regulate DNA replication and may function as a transcriptional coactivator (PubMed:12750254, PubMed:16387653). Inhibits cell growth, induces a delay in S-phase progression and enhances Fas-induced apoptosis in an INCA1-dependent manner (PubMed:21750715). {ECO:0000269|PubMed:12750254, ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:21750715}.; ",{"$nulls":4},"p.Met30Ile","c.90G>C","MODERATE","30/254",3,{"$nulls":5},"5","394","248","268","169","362","231","0","0","0","0.2727",{"$nulls":20},"3.068842",null,".;1.595;1.595","1",".;-3.58;-3.52",".;0.999;.",".;0.107;0.053",".;0.843;0.838",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","390,0","0","390","0/1","174,66","0.275","240",null,"chr2:241704699:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2959"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","INO80","chr15:40987118","INO80(L1269V)",null,null,"region of interest (Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: ATPase component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and DNA repair (PubMed:16230350, PubMed:16298340, PubMed:17721549, PubMed:20855601, PubMed:20237820). Binds DNA (PubMed:16298340, PubMed:21303910). As part of the INO80 complex, remodels chromatin by shifting nucleosomes (PubMed:16230350, PubMed:21303910). Regulates transcription upon recruitment by YY1 to YY1-activated genes, where it acts as an essential coactivator (PubMed:17721549). Involved in UV-damage excision DNA repair (PubMed:20855601). The contribution to DNA double-strand break repair appears to be largely indirect through transcriptional regulation (PubMed:20687897). Involved in DNA replication (PubMed:20237820). Required for microtubule assembly during mitosis thereby regulating chromosome segregation cycle (PubMed:20237820). {ECO:0000269|PubMed:16230350, ECO:0000269|PubMed:16298340, ECO:0000269|PubMed:17721549, ECO:0000269|PubMed:20237820, ECO:0000269|PubMed:20687897, ECO:0000269|PubMed:20855601, ECO:0000269|PubMed:21303910}.; ",{"$nulls":4},"p.Leu1269Val","c.3805C>G","MODERATE","1269/1556",31,{"$nulls":5},"5","545","794","395","569","457","679","0","0","0","0.2032",{"$nulls":20},"3.953952",".;3.17;3.17;.","2.085;2.085;2.085;.","1",".;-2.16;-2.16;.","0.993;0.993;0.993;.",".;0.006;0.006;.",".;0.544;0.53;0.576",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a subunit of the chromatin remodeling complex, which is classified into subfamilies depending on sequence features apart from the conserved ATPase domain. This protein is the catalytic ATPase subunit of the INO80 chromatin remodeling complex, which is characterized by a DNA-binding domain. This protein is proposed to bind DNA and be recruited by the YY1 transcription factor to activate certain genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013].",null,null,"0/0","526,0","0","526","0/1","618,149","0.1943","767",null,"chr15:40987118:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1828"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","INO80","chr15:40987118","INO80(L1269V)",null,null,"region of interest (Assembles INO80 complex module consisting of conserved components INO80B, INO80C, ACTR5, RVBL1, RVBL2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: ATPase component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and DNA repair (PubMed:16230350, PubMed:16298340, PubMed:17721549, PubMed:20855601, PubMed:20237820). Binds DNA (PubMed:16298340, PubMed:21303910). As part of the INO80 complex, remodels chromatin by shifting nucleosomes (PubMed:16230350, PubMed:21303910). Regulates transcription upon recruitment by YY1 to YY1-activated genes, where it acts as an essential coactivator (PubMed:17721549). Involved in UV-damage excision DNA repair (PubMed:20855601). The contribution to DNA double-strand break repair appears to be largely indirect through transcriptional regulation (PubMed:20687897). Involved in DNA replication (PubMed:20237820). Required for microtubule assembly during mitosis thereby regulating chromosome segregation cycle (PubMed:20237820). {ECO:0000269|PubMed:16230350, ECO:0000269|PubMed:16298340, ECO:0000269|PubMed:17721549, ECO:0000269|PubMed:20237820, ECO:0000269|PubMed:20687897, ECO:0000269|PubMed:20855601, ECO:0000269|PubMed:21303910}.; ",{"$nulls":4},"p.Leu1269Val","c.3805C>G","MODERATE","1269/1556",31,{"$nulls":5},"5","545","575","395","406","457","494","0","0","0","0.3016",{"$nulls":20},"3.953952",".;3.17;3.17;.","2.085;2.085;2.085;.","1",".;-2.16;-2.16;.","0.993;0.993;0.993;.",".;0.006;0.006;.",".;0.544;0.53;0.576",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a subunit of the chromatin remodeling complex, which is classified into subfamilies depending on sequence features apart from the conserved ATPase domain. This protein is the catalytic ATPase subunit of the INO80 chromatin remodeling complex, which is characterized by a DNA-binding domain. This protein is proposed to bind DNA and be recruited by the YY1 transcription factor to activate certain genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013].",null,null,"0/0","523,0","0","523","0/1","382,161","0.2965","543",null,"chr15:40987118:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2857"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","INPP5B","chr1:37862377","INPP5B(D974H)",null,null,"domain (Rho-GAP ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Hydrolyzes phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events. {ECO:0000269|PubMed:7721860}.; ",{"$nulls":4},"p.Asp974His","c.2920G>C","MODERATE","974/993",24,1,{"$nulls":4},"5","260","289","180","197","245","255","0","0","0","0.1725",{"$nulls":20},"3.426328","0.94",".;1.575;1.575;.","0.999778;0.999826;0.999826;0.999826","-1.37;-1.29;-1.29;-1.29",".;.;.;0.776","0.036;0.027;0.027;0.118","0.17;0.109;0.096;0.124",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","252,0","0","252","0/1","226,49","0.1782","275",null,"chr1:37862377:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1878"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ITGA10","chr1:145895357","ITGA10(H1051N)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs781997748",-1,null,"FUNCTION: Integrin alpha-10/beta-1 is a receptor for collagen.; ",{"$nulls":4},"p.His1051Asn","c.3151C>A","MODERATE","1051/1167",27,{"$nulls":5},"5","394","515","274","344","367","461","0","0","0","0.1171",{"$nulls":20},"1.594627","0.88",null,null,"0.54",null,"1.0","0.397;0.377",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Integrins are integral membrane proteins composed of an alpha chain and a beta chain, and are known to participate in cell adhesion as well as cell-surface mediated signalling. The I-domain containing alpha 10 combines with the integrin beta 1 chain (ITGB1) to form a novel collagen type II-binding integrin expressed in cartilage tissue. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","384,0","0","384","0/1","437,63","0.126","500",null,"chr1:145895357:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1134"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ITGA10","chr1:145895357","ITGA10(H1051N)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs781997748",-1,null,"FUNCTION: Integrin alpha-10/beta-1 is a receptor for collagen.; ",{"$nulls":4},"p.His1051Asn","c.3151C>A","MODERATE","1051/1167",27,{"$nulls":5},"5","394","294","274","199","364","255","0","0","0","0.2118",{"$nulls":20},"1.594627","0.88",null,null,"0.54",null,"1.0","0.397;0.377",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Integrins are integral membrane proteins composed of an alpha chain and a beta chain, and are known to participate in cell adhesion as well as cell-surface mediated signalling. The I-domain containing alpha 10 combines with the integrin beta 1 chain (ITGB1) to form a novel collagen type II-binding integrin expressed in cartilage tissue. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","377,0","0","377","0/1","217,65","0.2305","282",null,"chr1:145895357:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2312"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ITIH3","chr3:52796583","ITIH3(T73S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a carrier of hyaluronan in serum or as a binding protein between hyaluronan and other matrix protein, including those on cell surfaces in tissues to regulate the localization, synthesis and degradation of hyaluronan which are essential to cells undergoing biological processes.; ",{"$nulls":4},"p.Thr73Ser","c.217A>T","MODERATE","73/890",3,{"$nulls":5},"5","579","574","458","447","495","478","0","0","0","0.3159",{"$nulls":20},"-0.303549",".;1.98;1.98",".;.;1.02","1",".;-1.45;-1.16",".;0.003;0.013",".;0.632;0.528","0.089;0.073;0.08",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","570,0","0","570","0/1","380,176","0.3165","556",null,"chr3:52796583:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3154"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ITIH3","chr3:52796583","ITIH3(T73S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a carrier of hyaluronan in serum or as a binding protein between hyaluronan and other matrix protein, including those on cell surfaces in tissues to regulate the localization, synthesis and degradation of hyaluronan which are essential to cells undergoing biological processes.; ",{"$nulls":4},"p.Thr73Ser","c.217A>T","MODERATE","73/890",3,{"$nulls":5},"5","579","269","458","216","493","232","0","0","0","0.6767",{"$nulls":20},"-0.303549",".;1.98;1.98",".;.;1.02","1",".;-1.45;-1.16",".;0.003;0.013",".;0.632;0.528","0.089;0.073;0.08",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","571,0","0","571","0/1","90,177","0.6629","267",null,"chr3:52796583:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6667"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","KBTBD7","chr13:41192913","KBTBD7(V449I)",{"$nulls":6},255,"PASS","Missense","rs200426275",0.0006048,{"$nulls":6},"p.Val449Ile","c.1345G>A","MODERATE","449/684",1,{"$nulls":5},"5","715","414","580","323","571","326","0","0","0","0.0706",{"$nulls":20},"1.2254","-1.15","0.38","0.625073","-0.38","0.004","0.44","0.104",{"$nulls":3},"ExAC_FIN_AF",0.0006048,{"$nulls":7},"0/0","709,0","0","709","0/1","371,28","0.0702","399",null,"chr13:41192913:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.065"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KCNS1","chr20:45095338","KCNS1(H371Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Potassium channel subunit that does not form functional channels by itself. Can form functional heterotetrameric channels with KCNB1 and KCNB2; modulates the delayed rectifier voltage- gated potassium channel activation and deactivation rates of KCNB1 and KCNB2 (PubMed:10484328). {ECO:0000269|PubMed:10484328}.; ",{"$nulls":4},"p.His371Gln","c.1113C>G","MODERATE","371/526",5,{"$nulls":5},"5","277","332","211","248","235","278","0","0","0","0.1439",{"$nulls":20},"3.623563","-4.82","1.07","0.999757","-3.18","0.041","0.203","0.497;0.54",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","254,0","0","254","0/1","256,44","0.1467","300",null,"chr20:45095338:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1371"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KDM4A","chr1:43694729","KDM4A(K835N)",null,null,"zinc finger region (PHD-type 2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone demethylase that specifically demethylates 'Lys- 9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code (PubMed:26741168). Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively. {ECO:0000269|PubMed:16024779, ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:26741168}.; ",{"$nulls":4},"p.Lys835Asn","c.2505G>T","MODERATE","835/1064",18,{"$nulls":5},"3","395","449",null,null,"282","333","0","0","0","0.2042",{"$nulls":20},"3.712902","2.48","1.65","0.999316","-2.61","0.999","0.049","0.548",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009].  ",null,null,"0/0","391,0","0","391","0/1","365,76","0.1723","441",null,"chr1:43694729:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KDM5B","chr1:202745962","KDM5B(D776V)",null,null,"sequence variant (In MRT65. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:Q80Y84, ECO:0000269|PubMed:12657635, ECO:0000269|PubMed:16645588, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17363312, ECO:0000269|PubMed:24952722, ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:26741168, ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558}.; ",{"$nulls":4},"p.Asp776Val","c.2327A>T","MODERATE","776/1580",17,1,{"$nulls":4},"5","464","599","307","391","433","551","0","0","0","0.2577",{"$nulls":20},"4.243197","-2.4;.;-2.4;.;.;.;.;.;-2.4","2.25;.;.;.;.;.;.;.;.","1","-4.98;.;-4.98;.;.;.;.;.;-4.89","0.599;.;0.984;.;.;.;.;.;.","0.001;.;0.001;.;.;.;.;.;0.001","0.774;.;0.772;.;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748219","0/0","451,0","0","451","0/1","420,144","0.2553","564",null,"chr1:202745962:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2532"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","KDM5B","chr1:202745962","KDM5B(D776V)",null,null,"sequence variant (In MRT65. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:24952722, PubMed:27214403, PubMed:28262558). Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:Q80Y84, ECO:0000269|PubMed:12657635, ECO:0000269|PubMed:16645588, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17363312, ECO:0000269|PubMed:24952722, ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:26741168, ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558}.; ",{"$nulls":4},"p.Asp776Val","c.2327A>T","MODERATE","776/1580",17,1,{"$nulls":4},"5","464","269","307","185","416","245","0","0","0","0.6531",{"$nulls":20},"4.243197","-2.4;.;-2.4;.;.;.;.;.;-2.4","2.25;.;.;.;.;.;.;.;.","1","-4.98;.;-4.98;.;.;.;.;.;-4.89","0.599;.;0.984;.;.;.;.;.;.","0.001;.;0.001;.;.;.;.;.;0.001","0.774;.;0.772;.;.;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748219","0/0","457,0","0","457","0/1","91,173","0.6553","264",null,"chr1:202745962:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6649"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KIF4B","chr5:155015452","KIF4B(N531K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Motor protein that translocates PRC1 to the plus ends of interdigitating spindle microtubules during the metaphase to anaphase transition, an essential step for the formation of an organized central spindle midzone and midbody and for successful cytokinesis. May play a role in mitotic chromosomal positioning and bipolar spindle stabilization (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asn531Lys","c.1593C>G","MODERATE","531/1234",1,{"$nulls":5},"5","218","247","160","176","199","227","0","0","0","0.1366",{"$nulls":20},"-0.719137","-0.06","-3.075","0.998729","3.46",null,"1.0","0.076",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","217,1","0.0046","218","0/1","207,33","0.1375","240",null,"chr5:155015452:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1364"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KL","chr13:33016523","KL(G28A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Tumoral calcinosis, hyperphosphatemic, familial, 3 (HFTC3) [MIM:617994]: A form of hyperphosphatemic tumoral calcinosis, a rare autosomal recessive metabolic disorder that manifests with hyperphosphatemia and massive calcium deposits in the skin and subcutaneous tissues. Some patients have recurrent, transient, painful swellings of the long bones associated with the radiographic findings of periosteal reaction and cortical hyperostosis and absence of skin involvement. {ECO:0000269|PubMed:17710231}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May have weak glycosidase activity towards glucuronylated steroids. However, it lacks essential active site Glu residues at positions 239 and 872, suggesting it may be inactive as a glycosidase in vivo. May be involved in the regulation of calcium and phosphorus homeostasis by inhibiting the synthesis of active vitamin D (By similarity). Essential factor for the specific interaction between FGF23 and FGFR1 (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly28Ala","c.83G>C","MODERATE","28/1012",1,{"$nulls":5},"5","75","48","69","42","48","34","0","0","0","0.2941",{"$nulls":20},"0.879449","2.13",null,"1","0.1",null,"1.0","0.109",{"$nulls":3},"Unknown",-1,"AR","Tumoral calcinosis, hyperphosphatemic","Dermatologic; Musculoskeletal; Renal",{"$nulls":3},"C4693864","0/0","73,0","0","73","0/1","35,12","0.2553","47",null,"chr13:33016523:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2619"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","KL","chr13:33016523","KL(G28A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Tumoral calcinosis, hyperphosphatemic, familial, 3 (HFTC3) [MIM:617994]: A form of hyperphosphatemic tumoral calcinosis, a rare autosomal recessive metabolic disorder that manifests with hyperphosphatemia and massive calcium deposits in the skin and subcutaneous tissues. Some patients have recurrent, transient, painful swellings of the long bones associated with the radiographic findings of periosteal reaction and cortical hyperostosis and absence of skin involvement. {ECO:0000269|PubMed:17710231}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May have weak glycosidase activity towards glucuronylated steroids. However, it lacks essential active site Glu residues at positions 239 and 872, suggesting it may be inactive as a glycosidase in vivo. May be involved in the regulation of calcium and phosphorus homeostasis by inhibiting the synthesis of active vitamin D (By similarity). Essential factor for the specific interaction between FGF23 and FGFR1 (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly28Ala","c.83G>C","MODERATE","28/1012",1,{"$nulls":5},"4","75","32","69","29",null,null,"0","0",{"$nulls":22},"0.879449","2.13",null,"1","0.1",null,"1.0","0.109",{"$nulls":3},"Unknown",-1,"AR","Tumoral calcinosis, hyperphosphatemic","Dermatologic; Musculoskeletal; Renal",{"$nulls":3},"C4693864","0/0","73,0","0","73","0/1","15,16","0.5161","31",null,"chr13:33016523:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5172"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KLHL10","chr17:41845568","KLHL10(R376L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spermatogenic failure 11 (SPGF11) [MIM:615081]: An infertility disorder caused by spermatogenesis defects. It results in decreased sperm motility, concentration, and multiple sperm structural defects. Oligozoospermia is usually observed in SPGF11 patients. In addition to oligozoospermia, teratozoospermia and moderate asthenozoospermia is observed in some cases. {ECO:0000269|PubMed:17047026}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a substrate-specific adapter of a CUL3-based E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins during spermatogenesis.; ",{"$nulls":4},"p.Arg376Leu","c.1127G>T","MODERATE","376/608",3,{"$nulls":5},"4","781","912","609","683","701","826","0","0","0","0.1453",{"$nulls":20},"4.036157","-1.18","3.53","1","-6.72","1.0",null,"0.945",{"$nulls":3},"Unknown",-1,"AD","Spermatogenic failure 11","Genitourinary",{"$nulls":3},"C3554453","0/0","778,0","0","778","0/1","744,134","0.1526","878",null,"chr17:41845568:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1406"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","KLHL10","chr17:41845568","KLHL10(R376L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spermatogenic failure 11 (SPGF11) [MIM:615081]: An infertility disorder caused by spermatogenesis defects. It results in decreased sperm motility, concentration, and multiple sperm structural defects. Oligozoospermia is usually observed in SPGF11 patients. In addition to oligozoospermia, teratozoospermia and moderate asthenozoospermia is observed in some cases. {ECO:0000269|PubMed:17047026}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a substrate-specific adapter of a CUL3-based E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins during spermatogenesis.; ",{"$nulls":4},"p.Arg376Leu","c.1127G>T","MODERATE","376/608",3,{"$nulls":5},"5","781","786","609","623","701","692","0","0","0","0.3974",{"$nulls":20},"4.036157","-1.18","3.53","1","-6.72","1.0",null,"0.945",{"$nulls":3},"Unknown",-1,"AD","Spermatogenic failure 11","Genitourinary",{"$nulls":3},"C3554453","0/0","776,0","0","776","0/1","465,302","0.3937","767",null,"chr17:41845568:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3852"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","KRT72","chr12:52591500","KRT72(K309N)",null,null,"domain (IF rod ), region of interest (Coil 2 )",{"$nulls":3},255,"PASS","Missense","rs1293269267",-1,null,"FUNCTION: Has a role in hair formation. Specific component of keratin intermediate filaments in the inner root sheath (IRS) of the hair follicle (Probable). {ECO:0000305}.; ",{"$nulls":4},"p.Lys309Asn","c.927G>C","MODERATE","309/511",5,{"$nulls":5},"4","1046","1191","821","904","759","896","0","0","0","0.221",{"$nulls":20},"2.458761","-1.27;-1.27;-2.58","2.585","0.566943","-3.56;-3.56;-3.43","0.963;0.963;.","0.001","0.151;0.151;0.206",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1027,0","0","1027","0/1","920,238","0.2055","1158",null,"chr12:52591500:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2013"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","KRT72","chr12:52591500","KRT72(K309N)",null,null,"domain (IF rod ), region of interest (Coil 2 )",{"$nulls":3},255,"PASS","Missense","rs1293269267",-1,null,"FUNCTION: Has a role in hair formation. Specific component of keratin intermediate filaments in the inner root sheath (IRS) of the hair follicle (Probable). {ECO:0000305}.; ",{"$nulls":4},"p.Lys309Asn","c.927G>C","MODERATE","309/511",5,{"$nulls":5},"4","1046","1048","821","795","761","777","0","0","0","0.5174",{"$nulls":20},"2.458761","-1.27;-1.27;-2.58","2.585","0.566943","-3.56;-3.56;-3.43","0.963;0.963;.","0.001","0.151;0.151;0.206",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1022,0","0","1022","0/1","487,523","0.5178","1010",null,"chr12:52591500:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5082"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","KRT85","chr12:52360872","KRT85(R502P)",null,null,"region of interest (Tail )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Arg502Pro","c.1505G>C","MODERATE","502/507",9,{"$nulls":5},"4","411","593","317","466","342","502","0","0","0","0.0936",{"$nulls":20},"2.575952","-1.63;-1.54","1.965;.","0.857792","-2.41;-2.25","0.007;.","0.002;0.005","0.59;0.639",{"$nulls":3},"Unknown",-1,"AR","Ectodermal dysplasia 4, hair-nail type","Dermatologic",{"$nulls":3},"C1865951","0/0","403,0","0","403","0/1","518,58","0.1007","576",null,"chr12:52360872:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.103"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LARP7","chr4:112650490","LARP7(E449K)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Alazami syndrome (ALAZS) [MIM:615071]: A syndromic form of primordial dwarfism, a condition characterized by severe growth restriction that has its onset in utero, and results in short stature and undersize. ALAZS patients manifest severe intellectual disability and distinct facial features including malar hypoplasia, deep-set eyes, broad nose, short philtrum, and macrostomia. Some patients have non-specific and inconsistent skeletal findings, for example, scoliosis and mild epiphyseal changes in the proximal phalanges, but no frank dysplasia. {ECO:0000269|PubMed:21937992, ECO:0000269|PubMed:22865833}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. {ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18483487}.; ",{"$nulls":4},"p.Glu449Lys","c.1345G>A","MODERATE","449/589",12,{"$nulls":5},"5","235","212","175","154","196","166","0","0","0","0.1386",{"$nulls":20},"2.4908609999999998","2.16;2.15;.;2.16","1.825;.;.;1.825","0.976836","-1.62;-1.62;-1.36;-1.62","0.014;.;.;0.014","0.234;0.461;0.131;0.234","0.246;0.25;.;0.258",{"$nulls":3},"Unknown",-1,"AR","Alazami syndrome","Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C3554439","0|0","232,0","0","232","0|1","175,30","0.1463","205",null,"chr4:112650490:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1299"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LARP7","chr4:112650490","LARP7(E449K)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Alazami syndrome (ALAZS) [MIM:615071]: A syndromic form of primordial dwarfism, a condition characterized by severe growth restriction that has its onset in utero, and results in short stature and undersize. ALAZS patients manifest severe intellectual disability and distinct facial features including malar hypoplasia, deep-set eyes, broad nose, short philtrum, and macrostomia. Some patients have non-specific and inconsistent skeletal findings, for example, scoliosis and mild epiphyseal changes in the proximal phalanges, but no frank dysplasia. {ECO:0000269|PubMed:21937992, ECO:0000269|PubMed:22865833}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. {ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18483487}.; ",{"$nulls":4},"p.Glu449Lys","c.1345G>A","MODERATE","449/589",12,{"$nulls":5},"5","235","125","175","91","193","99","0","0","0","0.2929",{"$nulls":20},"2.4908609999999998","2.16;2.15;.;2.16","1.825;.;.;1.825","0.976836","-1.62;-1.62;-1.36;-1.62","0.014;.;.;0.014","0.234;0.461;0.131;0.234","0.246;0.25;.;0.258",{"$nulls":3},"Unknown",-1,"AR","Alazami syndrome","Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C3554439","0|0","233,0","0","233","0|1","81,34","0.2957","115",null,"chr4:112650490:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2967"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LARP7","chr4:112650492","LARP7(V451fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Alazami syndrome (ALAZS) [MIM:615071]: A syndromic form of primordial dwarfism, a condition characterized by severe growth restriction that has its onset in utero, and results in short stature and undersize. ALAZS patients manifest severe intellectual disability and distinct facial features including malar hypoplasia, deep-set eyes, broad nose, short philtrum, and macrostomia. Some patients have non-specific and inconsistent skeletal findings, for example, scoliosis and mild epiphyseal changes in the proximal phalanges, but no frank dysplasia. {ECO:0000269|PubMed:21937992, ECO:0000269|PubMed:22865833}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. {ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18483487}.; ",{"$nulls":4},"p.Val451fs","c.1350delA","HIGH","450/589",12,{"$nulls":5},"5","240","217","177","162","208","186","0","0","0","0.1129",{"$nulls":5},"(LARP7|ENSG00000174720|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Alazami syndrome","Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C3554439","0|0","234,0","0","234","0|1","175,30","0.1463","205",null,"chr4:112650492:GA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1358"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LARP7","chr4:112650492","LARP7(V451fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Alazami syndrome (ALAZS) [MIM:615071]: A syndromic form of primordial dwarfism, a condition characterized by severe growth restriction that has its onset in utero, and results in short stature and undersize. ALAZS patients manifest severe intellectual disability and distinct facial features including malar hypoplasia, deep-set eyes, broad nose, short philtrum, and macrostomia. Some patients have non-specific and inconsistent skeletal findings, for example, scoliosis and mild epiphyseal changes in the proximal phalanges, but no frank dysplasia. {ECO:0000269|PubMed:21937992, ECO:0000269|PubMed:22865833}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. {ECO:0000269|PubMed:18249148, ECO:0000269|PubMed:18483487}.; ",{"$nulls":4},"p.Val451fs","c.1350delA","HIGH","450/589",12,{"$nulls":5},"5","240","125","177","95","207","104","0","0","0","0.2596",{"$nulls":5},"(LARP7|ENSG00000174720|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Alazami syndrome","Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C3554439","0|0","235,0","0","235","0|1","83,34","0.2906","117",null,"chr4:112650492:GA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2842"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LCE2A","chr1:152698912","LCE2A(Q4L)",null,null,"compositionally biased region (Cys-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Precursors of the cornified envelope of the stratum corneum.; ",{"$nulls":4},"p.Gln4Leu","c.11A>T","MODERATE","4/106",2,{"$nulls":5},"5","317","222","243","172","213","135","0","0","0","0.1481",{"$nulls":20},"3.425004","3.42","3.465","0.94605","-7.0","0.999",null,"0.499",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","313,0","0","313","0/1","174,34","0.1635","208",null,"chr1:152698912:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.157"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LIMCH1","chr4:41676410","LIMCH1(E1156G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration. {ECO:0000269|PubMed:28228547}.; ",{"$nulls":4},"p.Glu1156Gly","c.3467A>G","MODERATE","1156/1467",23,{"$nulls":5},"5","258","210","184","161","217","178","0","0","0","0.2697",{"$nulls":20},"4.70351","0.58",".;.;2.48;2.48;.;.;.;.;.;.;.","0.999762;0.999762;0.999762;0.999762;0.999762;0.999762;0.999047;0.999047;0.999047;0.999047;0.999762;1","-5.57;-5.39;-5.39;-5.39;-5.57;-5.16;-5.15;-5.15;-5.38;-5.15;-5.38","1.0;.;1.0;1.0;1.0;0.995;.;0.999;1.0;1.0;1.0","0.001;0.0;0.0;0.0;0.001;0.0;0.0;0.001;0.001;0.0;0.001","0.82;0.703;0.72;0.652;0.75;0.735;0.791;0.801;0.805;0.803;0.796",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","253,0","0","253","0/1","144,56","0.28","200",null,"chr4:41676410:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2671"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LIMCH1","chr4:41676410","LIMCH1(E1156G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration. {ECO:0000269|PubMed:28228547}.; ",{"$nulls":4},"p.Glu1156Gly","c.3467A>G","MODERATE","1156/1467",23,{"$nulls":5},"5","258","91","184","71","216","77","0","0","0","0.7143",{"$nulls":20},"4.70351","0.58",".;.;2.48;2.48;.;.;.;.;.;.;.","0.999762;0.999762;0.999762;0.999762;0.999762;0.999762;0.999047;0.999047;0.999047;0.999047;0.999762;1","-5.57;-5.39;-5.39;-5.39;-5.57;-5.16;-5.15;-5.15;-5.38;-5.15;-5.38","1.0;.;1.0;1.0;1.0;0.995;.;0.999;1.0;1.0;1.0","0.001;0.0;0.0;0.0;0.001;0.0;0.0;0.001;0.001;0.0;0.001","0.82;0.703;0.72;0.652;0.75;0.735;0.791;0.801;0.805;0.803;0.796",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","254,0","0","254","0/1","28,60","0.6818","88",null,"chr4:41676410:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7042"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LOX","chr5:122074068","LOX(D327G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Aortic aneurysm, familial thoracic 10 (AAT10) [MIM:617168]: A form of thoracic aortic aneurysm, a disease characterized by permanent dilation of the thoracic aorta usually due to degenerative changes in the aortic wall. It is primarily associated with a characteristic histologic appearance known as 'medial necrosis' or 'Erdheim cystic medial necrosis' in which there is degeneration and fragmentation of elastic fibers, loss of smooth muscle cells, and an accumulation of basophilic ground substance. {ECO:0000269|PubMed:26838787, ECO:0000269|PubMed:27432961}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Responsible for the post-translational oxidative deamination of peptidyl lysine residues in precursors to fibrous collagen and elastin (PubMed:26838787). Regulator of Ras expression. May play a role in tumor suppression. Plays a role in the aortic wall architecture (By similarity). {ECO:0000250|UniProtKB:P28301, ECO:0000269|PubMed:26838787}.; ",{"$nulls":4},"p.Asp327Gly","c.980A>G","MODERATE","327/417",4,{"$nulls":5},"5","511","569","382","411","433","476","0","0","0","0.1534",{"$nulls":20},"4.481973","0.91;.","3.405","1","-6.97;.","1.0","0.0;.","0.954;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4284414","0/0","495,0","0","495","0/1","467,80","0.1463","547",null,"chr5:122074068:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1411"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LRBA","chr4:150315567","LRBA(L2574V)",{"$nulls":6},255,"PASS","Missense","rs202014892",1.1627906976744188E-4,"DISEASE: Immunodeficiency, common variable, 8, with autoimmunity (CVID8) [MIM:614700]: An autosomal recessive immunologic disorder associated with defective B-cell differentiation and decreased or absent antibody production. Affected individuals have early- childhood onset of recurrent infections, particularly respiratory infections, and also develop variable autoimmune disorders, including idiopathic thrombocytopenic purpura, autoimmune hemolytic anemia, and inflammatory bowel disease. {ECO:0000269|PubMed:22608502}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be involved in coupling signal transduction and vesicle trafficking to enable polarized secretion and/or membrane deposition of immune effector molecules. {ECO:0000250}.; ",{"$nulls":4},"p.Leu2574Val","c.7720C>G","MODERATE","2574/2863",52,{"$nulls":5},"5","273","291","190","198","219","242","0","0","0","0.4008",{"$nulls":20},"2.473858","-0.55;-0.55;.;0.25",".;1.665;.;.","0.999999;0.999999;0.999993;0.999999","-1.18;-1.18;.;-1.3","0.119;0.642;.;.","0.471;0.449;.;0.386","0.487;0.486;.;0.316",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,"AR","Common variable immunodeficiency 8, with autoimmunity","Allergy/Immunology/Infectious; Cardiovascular; Endocrine; Hematologic",{"$nulls":3},"C3553512","0/0","269,0","0","269","0/1","171,103","0.3759","274",null,"chr4:150315567:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3687"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LRBA","chr4:150315567","LRBA(L2574V)",{"$nulls":6},255,"PASS","Missense","rs202014892",1.1627906976744188E-4,"DISEASE: Immunodeficiency, common variable, 8, with autoimmunity (CVID8) [MIM:614700]: An autosomal recessive immunologic disorder associated with defective B-cell differentiation and decreased or absent antibody production. Affected individuals have early- childhood onset of recurrent infections, particularly respiratory infections, and also develop variable autoimmune disorders, including idiopathic thrombocytopenic purpura, autoimmune hemolytic anemia, and inflammatory bowel disease. {ECO:0000269|PubMed:22608502}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be involved in coupling signal transduction and vesicle trafficking to enable polarized secretion and/or membrane deposition of immune effector molecules. {ECO:0000250}.; ",{"$nulls":4},"p.Leu2574Val","c.7720C>G","MODERATE","2574/2863",52,{"$nulls":5},"5","273","114","190","82","220","100","0","0","0","0.69",{"$nulls":20},"2.473858","-0.55;-0.55;.;0.25",".;1.665;.;.","0.999999;0.999999;0.999993;0.999999","-1.18;-1.18;.;-1.3","0.119;0.642;.;.","0.471;0.449;.;0.386","0.487;0.486;.;0.316",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,"AR","Common variable immunodeficiency 8, with autoimmunity","Allergy/Immunology/Infectious; Cardiovascular; Endocrine; Hematologic",{"$nulls":3},"C3553512","0/0","272,0","0","272","0/1","34,76","0.6909","110",null,"chr4:150315567:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6829"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LRFN5","chr14:41887448","LRFN5(W275G)",null,null,"topological domain (Extracellular ), domain (LRRCT ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell adhesion molecule that mediates homophilic cell- cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons. {ECO:0000269|PubMed:18227064, ECO:0000269|PubMed:18585462}.; ","tcga-gbm",{"$nulls":3},"p.Trp275Gly","c.823T>G","MODERATE","275/719",3,{"$nulls":5},"5","699","670","523","495","638","600","0","0","0","0.28",{"$nulls":20},"4.289341","0.71","1.87;.;.","0.999996","-12.56;-12.72;-12.72","1.0;.;1.0","0.01;0.036;0.033","0.851;0.837;0.824",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","692,0","0","692","0/1","466,178","0.2764","644",null,"chr14:41887448:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2667"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LRFN5","chr14:41887448","LRFN5(W275G)",null,null,"topological domain (Extracellular ), domain (LRRCT ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell adhesion molecule that mediates homophilic cell- cell adhesion in a Ca(2+)-independent manner. Promotes neurite outgrowth in hippocampal neurons. {ECO:0000269|PubMed:18227064, ECO:0000269|PubMed:18585462}.; ","tcga-gbm",{"$nulls":3},"p.Trp275Gly","c.823T>G","MODERATE","275/719",3,{"$nulls":5},"5","699","329","523","254","639","284","0","0","0","0.5951",{"$nulls":20},"4.289341","0.71","1.87;.;.","0.999996","-12.56;-12.72;-12.72","1.0;.;1.0","0.01;0.036;0.033","0.851;0.837;0.824",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","693,0","0","693","0/1","125,192","0.6057","317",null,"chr14:41887448:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6181"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LRIG2","chr1:113110317","LRIG2(T518R)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr518Arg","c.1553C>G","MODERATE","518/1065",13,{"$nulls":5},"5","330","462","253","350","279","390","0","0","0","0.0846",{"$nulls":20},"1.215958","2.47","0.725","0.905812","-4.09","0.043","0.064","0.381",{"$nulls":3},"Unknown",-1,"AR","Urofacial syndrome 2","Craniofacial; Renal",{"$nulls":3},"C3554520","0/0","320,0","0","320","0/1","404,39","0.088","443",null,"chr1:113110317:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0857"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LRIG2","chr1:113110317","LRIG2(T518R)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr518Arg","c.1553C>G","MODERATE","518/1065",13,{"$nulls":5},"5","330","294","253","236","280","255","0","0","0","0.1804",{"$nulls":20},"1.215958","2.47","0.725","0.905812","-4.09","0.043","0.064","0.381",{"$nulls":3},"Unknown",-1,"AR","Urofacial syndrome 2","Craniofacial; Renal",{"$nulls":3},"C3554520","0/0","318,0","0","318","0/1","235,52","0.1812","287",null,"chr1:113110317:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1695"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LRRK2","chr12:40295645","LRRK2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss","rs1448314911",-1,"DISEASE: Parkinson disease 8 (PARK8) [MIM:607060]: A slowly progressive neurodegenerative disorder characterized by bradykinesia, rigidity, resting tremor, postural instability, neuronal loss in the substantia nigra, and the presence of neurofibrillary MAPT (tau)-positive and Lewy bodies in some patients. {ECO:0000269|PubMed:15541308, ECO:0000269|PubMed:15541309, ECO:0000269|PubMed:15680455, ECO:0000269|PubMed:15680456, ECO:0000269|PubMed:15680457, ECO:0000269|PubMed:15726496, ECO:0000269|PubMed:15732108, ECO:0000269|PubMed:15811454, ECO:0000269|PubMed:15852371, ECO:0000269|PubMed:15880653, ECO:0000269|PubMed:15925109, ECO:0000269|PubMed:15929036, ECO:0000269|PubMed:16102999, ECO:0000269|PubMed:16157901, ECO:0000269|PubMed:16157908, ECO:0000269|PubMed:16157909, ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:16240353, ECO:0000269|PubMed:16247070, ECO:0000269|PubMed:16250030, ECO:0000269|PubMed:16251215, ECO:0000269|PubMed:16269541, ECO:0000269|PubMed:16272164, ECO:0000269|PubMed:16272257, ECO:0000269|PubMed:16298482, ECO:0000269|PubMed:16321986, ECO:0000269|PubMed:16333314, ECO:0000269|PubMed:16533964, ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18213618, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22956510, ECO:0000269|PubMed:23395371}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Positively regulates autophagy through a calcium- dependent activation of the CaMKK/AMPK signaling pathway. The process involves activation of nicotinic acid adenine dinucleotide phosphate (NAADP) receptors, increase in lysosomal pH, and calcium release from lysosomes. Together with RAB29, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner. Regulates neuronal process morphology in the intact central nervous system (CNS). Plays a role in synaptic vesicle trafficking. Phosphorylates PRDX3. Has GTPase activity. May play a role in the phosphorylation of proteins central to Parkinson disease. {ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18230735, ECO:0000269|PubMed:20949042, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22012985, ECO:0000269|PubMed:23395371, ECO:0000269|PubMed:24687852}.; ",{"$nulls":5},"c.3096+1G>A","HIGH",null,23,{"$nulls":5},"3","52","73","44","61",null,null,"0","0",{"$nulls":7},"(LRRK2|ENSG00000188906|1|1.00)",{"$nulls":14},"5.070432",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Parkinson disease 8; Dementia, Lewy body","Neurologic",{"$nulls":3},"C1846862","0/0","51,0","0","51","0/1","50,23","0.3151","73",null,"chr12:40295645:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3443"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LRRK2","chr12:40295645","LRRK2(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss","rs1448314911",-1,"DISEASE: Parkinson disease 8 (PARK8) [MIM:607060]: A slowly progressive neurodegenerative disorder characterized by bradykinesia, rigidity, resting tremor, postural instability, neuronal loss in the substantia nigra, and the presence of neurofibrillary MAPT (tau)-positive and Lewy bodies in some patients. {ECO:0000269|PubMed:15541308, ECO:0000269|PubMed:15541309, ECO:0000269|PubMed:15680455, ECO:0000269|PubMed:15680456, ECO:0000269|PubMed:15680457, ECO:0000269|PubMed:15726496, ECO:0000269|PubMed:15732108, ECO:0000269|PubMed:15811454, ECO:0000269|PubMed:15852371, ECO:0000269|PubMed:15880653, ECO:0000269|PubMed:15925109, ECO:0000269|PubMed:15929036, ECO:0000269|PubMed:16102999, ECO:0000269|PubMed:16157901, ECO:0000269|PubMed:16157908, ECO:0000269|PubMed:16157909, ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:16240353, ECO:0000269|PubMed:16247070, ECO:0000269|PubMed:16250030, ECO:0000269|PubMed:16251215, ECO:0000269|PubMed:16269541, ECO:0000269|PubMed:16272164, ECO:0000269|PubMed:16272257, ECO:0000269|PubMed:16298482, ECO:0000269|PubMed:16321986, ECO:0000269|PubMed:16333314, ECO:0000269|PubMed:16533964, ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18213618, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22956510, ECO:0000269|PubMed:23395371}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Positively regulates autophagy through a calcium- dependent activation of the CaMKK/AMPK signaling pathway. The process involves activation of nicotinic acid adenine dinucleotide phosphate (NAADP) receptors, increase in lysosomal pH, and calcium release from lysosomes. Together with RAB29, plays a role in the retrograde trafficking pathway for recycling proteins, such as mannose 6 phosphate receptor (M6PR), between lysosomes and the Golgi apparatus in a retromer-dependent manner. Regulates neuronal process morphology in the intact central nervous system (CNS). Plays a role in synaptic vesicle trafficking. Phosphorylates PRDX3. Has GTPase activity. May play a role in the phosphorylation of proteins central to Parkinson disease. {ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18230735, ECO:0000269|PubMed:20949042, ECO:0000269|PubMed:21850687, ECO:0000269|PubMed:22012985, ECO:0000269|PubMed:23395371, ECO:0000269|PubMed:24687852}.; ",{"$nulls":5},"c.3096+1G>A","HIGH",null,23,{"$nulls":5},"3","52","48","44","42",null,null,"0","0",{"$nulls":7},"(LRRK2|ENSG00000188906|1|1.00)",{"$nulls":14},"5.070432",null,null,"1",{"$nulls":7},"Unknown",-1,"AD","Parkinson disease 8; Dementia, Lewy body","Neurologic",{"$nulls":3},"C1846862","0/0","51,0","0","51","0/1","27,21","0.4375","48",null,"chr12:40295645:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4762"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LUC7L","chr16:190559","LUC7L(R263T)",null,null,"compositionally biased region (Arg/Ser-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May bind to RNA via its Arg/Ser-rich domain. {ECO:0000269|PubMed:11170747}.; ",{"$nulls":4},"p.Arg263Thr","c.788G>C","MODERATE","263/371",8,{"$nulls":5},"5","362","373","238","248","325","332","0","0","0","0.3705",{"$nulls":20},"2.422255",".;1.02;1.02;0.56;2.9;.","2.085;2.085;2.085;.;.;.","0.999991;0.999991;0.999991;0.999996","-2.25;-2.12;-2.12;-3.51;-2.22;-2.41","0.18;.;.;.;.;.","0.048;0.019;0.019;0.014;0.017;0.015","0.464;0.438;0.438;.;0.459;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","343,0","0","343","0/1","212,129","0.3783","341",null,"chr16:190559:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3629"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LUC7L","chr16:190559","LUC7L(R263T)",null,null,"compositionally biased region (Arg/Ser-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May bind to RNA via its Arg/Ser-rich domain. {ECO:0000269|PubMed:11170747}.; ",{"$nulls":4},"p.Arg263Thr","c.788G>C","MODERATE","263/371",8,{"$nulls":5},"5","362","246","238","162","326","220","0","0","0","0.7909",{"$nulls":20},"2.422255",".;1.02;1.02;0.56;2.9;.","2.085;2.085;2.085;.;.;.","0.999991;0.999991;0.999991;0.999996","-2.25;-2.12;-2.12;-3.51;-2.22;-2.41","0.18;.;.;.;.;.","0.048;0.019;0.019;0.014;0.017;0.015","0.464;0.438;0.438;.;0.459;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","341,0","0","341","0/1","47,180","0.793","227",null,"chr16:190559:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.784"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","LZTS2","chr10:101003791","LZTS2(Y231*)",null,null,"region of interest (Required for centrosomal localization ), compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Negative regulator of katanin-mediated microtubule severing and release from the centrosome. Required for central spindle formation and the completion of cytokinesis. May negatively regulate axonal outgrowth by preventing the formation of microtubule bundles that are necessary for transport within the elongating axon. Negative regulator of the Wnt signaling pathway. Represses beta-catenin-mediated transcriptional activation by promoting the nuclear exclusion of beta-catenin. {ECO:0000255|HAMAP-Rule:MF_03026, ECO:0000269|PubMed:17000760, ECO:0000269|PubMed:17351128, ECO:0000269|PubMed:17950943, ECO:0000269|PubMed:18490357}.; ",{"$nulls":4},"p.Tyr231*","c.693C>G","HIGH","231/669",2,{"$nulls":5},"4","939","856","687","604","811","726","0","0","0","0.2452",{"$nulls":5},"(LZTS2|ENSG00000107816|1|1.00)","(LZTS2|ENSG00000107816|1|1.00)",{"$nulls":13},"6.352217",null,null,"1",{"$nulls":3},".;0.28;0.28",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","932,0","0","932","0/1","620,203","0.2467","823",null,"chr10:101003791:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2517"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","LZTS2","chr10:101003791","LZTS2(Y231*)",null,null,"region of interest (Required for centrosomal localization ), compositionally biased region (Ser-rich )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Negative regulator of katanin-mediated microtubule severing and release from the centrosome. Required for central spindle formation and the completion of cytokinesis. May negatively regulate axonal outgrowth by preventing the formation of microtubule bundles that are necessary for transport within the elongating axon. Negative regulator of the Wnt signaling pathway. Represses beta-catenin-mediated transcriptional activation by promoting the nuclear exclusion of beta-catenin. {ECO:0000255|HAMAP-Rule:MF_03026, ECO:0000269|PubMed:17000760, ECO:0000269|PubMed:17351128, ECO:0000269|PubMed:17950943, ECO:0000269|PubMed:18490357}.; ",{"$nulls":4},"p.Tyr231*","c.693C>G","HIGH","231/669",2,{"$nulls":5},"4","939","323","687","243","806","280","0","0","0","0.5357",{"$nulls":5},"(LZTS2|ENSG00000107816|1|1.00)","(LZTS2|ENSG00000107816|1|1.00)",{"$nulls":13},"6.352217",null,null,"1",{"$nulls":3},".;0.28;0.28",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","934,0","0","934","0/1","145,173","0.544","318",null,"chr10:101003791:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.535"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MACF1","chr1:39350937","MACF1(E3743D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform 2: F-actin-binding protein which plays a role in cross-linking actin to other cytoskeletal proteins and also binds to microtubules (PubMed:15265687, PubMed:20937854). Plays an important role in ERBB2-dependent stabilization of microtubules at the cell cortex (PubMed:20937854). Acts as a positive regulator of Wnt receptor signaling pathway and is involved in the translocation of AXIN1 and its associated complex (composed of APC, CTNNB1 and GSK3B) from the cytoplasm to the cell membrane (By similarity). Has actin-regulated ATPase activity and is essential for controlling focal adhesions (FAs) assembly and dynamics (By similarity). Interaction with CAMSAP3 at the minus ends of non- centrosomal microtubules tethers microtubules minus-ends to actin filaments, regulating focal adhesion size and cell migration (PubMed:27693509). May play role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with GOLGA4 (PubMed:15265687). Plays a key role in wound healing and epidermal cell migration (By similarity). Required for efficient upward migration of bulge cells in response to wounding and this function is primarily rooted in its ability to coordinate microtubule dynamics and polarize hair follicle stem cells (By similarity). {ECO:0000250|UniProtKB:Q9QXZ0, ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:20937854, ECO:0000269|PubMed:27693509}.; ",{"$nulls":4},"p.Glu3743Asp","c.11229G>C","MODERATE","3743/7592",43,{"$nulls":5},"5","422","394","301","295","372","347","0","0","0","0.1354",{"$nulls":20},"1.433578","0.06;0.11;1.32;-0.09;1.32;1.21",null,"0.999625;0.998722;0.999982;0.999494;0.999625;0.999982;0.999982;0.982328","-1.92;-2.2;-1.93;-1.92;-0.88;-1.96",".;0.865;0.337;.;.;.","0.074;0.208;0.159;0.072;0.108;0.071","0.296;0.288;0.272;0.294;.;0.283",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5193029","0/0","414,0","0","414","0/1","329,57","0.1477","386",null,"chr1:39350937:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1525"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MAD1L1","chr7:2217973","MAD1L1(Q223*)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Defects in MAD1L1 are involved in the development and/or progression of various types of cancer. {ECO:0000269|PubMed:10597320, ECO:0000269|PubMed:11423979}.; ","FUNCTION: Component of the spindle-assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. May recruit MAD2L1 to unattached kinetochores. Has a role in the correct positioning of the septum. Required for anchoring MAD2L1 to the nuclear periphery. Binds to the TERT promoter and represses telomerase expression, possibly by interfering with MYC binding. {ECO:0000269|PubMed:10049595, ECO:0000269|PubMed:12837246, ECO:0000269|PubMed:20133940}.; ","level2",{"$nulls":3},"p.Gln223*","c.667C>T","HIGH","223/718",5,{"$nulls":5},"4","287","376","215","272","236","305","0","0","0","0.2852",{"$nulls":5},"(MAD1L1|ENSG00000002822|1|1.00)","(MAD1L1|ENSG00000002822|1|1.00)",{"$nulls":13},"8.627715",null,null,"1",{"$nulls":3},"0.884;0.885;0.883;0.883;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE",null,null,"C0376358","0/0","273,0","0","273","0/1","258,94","0.267","352",null,"chr7:2217973:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.261"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MAD1L1","chr7:2217973","MAD1L1(Q223*)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Defects in MAD1L1 are involved in the development and/or progression of various types of cancer. {ECO:0000269|PubMed:10597320, ECO:0000269|PubMed:11423979}.; ","FUNCTION: Component of the spindle-assembly checkpoint that prevents the onset of anaphase until all chromosomes are properly aligned at the metaphase plate. May recruit MAD2L1 to unattached kinetochores. Has a role in the correct positioning of the septum. Required for anchoring MAD2L1 to the nuclear periphery. Binds to the TERT promoter and represses telomerase expression, possibly by interfering with MYC binding. {ECO:0000269|PubMed:10049595, ECO:0000269|PubMed:12837246, ECO:0000269|PubMed:20133940}.; ","level2",{"$nulls":3},"p.Gln223*","c.667C>T","HIGH","223/718",5,{"$nulls":5},"4","287","188","215","136","236","152","0","0","0","0.2105",{"$nulls":5},"(MAD1L1|ENSG00000002822|1|1.00)","(MAD1L1|ENSG00000002822|1|1.00)",{"$nulls":13},"8.627715",null,null,"1",{"$nulls":3},"0.884;0.885;0.883;0.883;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE",null,null,"C0376358","0/0","271,0","0","271","0/1","133,37","0.2176","170",null,"chr7:2217973:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1912"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MAFB","chr20:40688017","MAFB(E278D)",null,null,"domain (bZIP ), region of interest (Leucine-zipper )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Multicentric carpotarsal osteolysis syndrome (MCTO) [MIM:166300]: A rare skeletal disorder, usually presenting in early childhood with a clinical picture mimicking juvenile rheumatoid arthritis. Progressive destruction of the carpal and tarsal bone usually occurs and other bones may also be involved. Chronic renal failure is a frequent component of the syndrome. Mental retardation and minor facial anomalies have been noted in some patients. {ECO:0000269|PubMed:22387013}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Duane retraction syndrome 3 with or without deafness (DURS3) [MIM:617041]: A form of Duane retraction syndrome, a congenital eye movement disorder characterized by a failure of cranial nerve VI (the abducens nerve) to develop normally, resulting in restriction or absence of abduction, adduction or both, narrowing of the palpebral fissure, and retraction of the globe on attempted adduction. Undiagnosed in children, it can lead to amblyopia, a permanent uncorrectable loss of vision. Some DURS3 patients manifest sensorineural hearing loss. {ECO:0000269|PubMed:27181683}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a transcriptional activator or repressor (PubMed:27181683). Plays a pivotal role in regulating lineage- specific hematopoiesis by repressing ETS1-mediated transcription of erythroid-specific genes in myeloid cells. Required for monocytic, macrophage, osteoclast, podocyte and islet beta cell differentiation. Involved in renal tubule survival and F4/80 maturation. Activates the insulin and glucagon promoters. Together with PAX6, transactivates weakly the glucagon gene promoter through the G1 element. SUMO modification controls its transcriptional activity and ability to specify macrophage fate. Binds element G1 on the glucagon promoter (By similarity). Involved either as an oncogene or as a tumor suppressor, depending on the cell context. {ECO:0000250|UniProtKB:P54841, ECO:0000269|PubMed:19143053, ECO:0000269|PubMed:27181683}.; ","gedi|level2",{"$nulls":3},"p.Glu278Asp","c.834G>C","MODERATE","278/323",1,{"$nulls":5},"4","477","596","365","425","412","517","0","0","0","0.236",{"$nulls":20},"2.612295","-2.89","1.35","0.999998","-0.74","0.157","0.538","0.237",{"$nulls":3},"Unknown",-1,"AD","Multicentric carpotarsal osteolysis","Craniofacial; Musculoskeletal; Renal","COSMIC","The protein encoded by this gene is a basic leucine zipper (bZIP) transcription factor that plays an important role in the regulation of lineage-specific hematopoiesis. The encoded nuclear protein represses ETS1-mediated transcription of erythroid-specific genes in myeloid cells. This gene contains no introns. [provided by RefSeq, Jul 2008].  ",null,"C4310752| C2674705","0/0","464,0","0","464","0/1","418,132","0.24","550",null,"chr20:40688017:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2471"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MAFB","chr20:40688017","MAFB(E278D)",null,null,"domain (bZIP ), region of interest (Leucine-zipper )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Multicentric carpotarsal osteolysis syndrome (MCTO) [MIM:166300]: A rare skeletal disorder, usually presenting in early childhood with a clinical picture mimicking juvenile rheumatoid arthritis. Progressive destruction of the carpal and tarsal bone usually occurs and other bones may also be involved. Chronic renal failure is a frequent component of the syndrome. Mental retardation and minor facial anomalies have been noted in some patients. {ECO:0000269|PubMed:22387013}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Duane retraction syndrome 3 with or without deafness (DURS3) [MIM:617041]: A form of Duane retraction syndrome, a congenital eye movement disorder characterized by a failure of cranial nerve VI (the abducens nerve) to develop normally, resulting in restriction or absence of abduction, adduction or both, narrowing of the palpebral fissure, and retraction of the globe on attempted adduction. Undiagnosed in children, it can lead to amblyopia, a permanent uncorrectable loss of vision. Some DURS3 patients manifest sensorineural hearing loss. {ECO:0000269|PubMed:27181683}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a transcriptional activator or repressor (PubMed:27181683). Plays a pivotal role in regulating lineage- specific hematopoiesis by repressing ETS1-mediated transcription of erythroid-specific genes in myeloid cells. Required for monocytic, macrophage, osteoclast, podocyte and islet beta cell differentiation. Involved in renal tubule survival and F4/80 maturation. Activates the insulin and glucagon promoters. Together with PAX6, transactivates weakly the glucagon gene promoter through the G1 element. SUMO modification controls its transcriptional activity and ability to specify macrophage fate. Binds element G1 on the glucagon promoter (By similarity). Involved either as an oncogene or as a tumor suppressor, depending on the cell context. {ECO:0000250|UniProtKB:P54841, ECO:0000269|PubMed:19143053, ECO:0000269|PubMed:27181683}.; ","gedi|level2",{"$nulls":3},"p.Glu278Asp","c.834G>C","MODERATE","278/323",1,{"$nulls":5},"4","477","423","365","320","412","355","0","0","0","0.4225",{"$nulls":20},"2.612295","-2.89","1.35","0.999998","-0.74","0.157","0.538","0.237",{"$nulls":3},"Unknown",-1,"AD","Multicentric carpotarsal osteolysis","Craniofacial; Musculoskeletal; Renal","COSMIC","The protein encoded by this gene is a basic leucine zipper (bZIP) transcription factor that plays an important role in the regulation of lineage-specific hematopoiesis. The encoded nuclear protein represses ETS1-mediated transcription of erythroid-specific genes in myeloid cells. This gene contains no introns. [provided by RefSeq, Jul 2008].  ",null,"C4310752| C2674705","0/0","473,0","0","473","0/1","247,163","0.3976","410",null,"chr20:40688017:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4062"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MAMDC2","chr9:70218559","MAMDC2(R625Q)",{"$nulls":6},255,"PASS","Missense","rs79468073",0.01929187471629596,{"$nulls":6},"p.Arg625Gln","c.1874G>A","MODERATE","625/686",12,{"$nulls":5},"5","265","290","204","213","243","265","0","0","0","0.2528",{"$nulls":20},"1.8473410000000001","4.46","0.73","0.998602","-0.78","0.432","0.245","0.231",{"$nulls":3},"ESP6500_AA_AF",0.01929187471629596,{"$nulls":7},"0/0","262,0","0","262","0/1","214,68","0.2411","282",null,"chr9:70218559:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.23"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MAMDC2","chr9:70218559","MAMDC2(R625Q)",{"$nulls":6},255,"PASS","Missense","rs79468073",0.01929187471629596,{"$nulls":6},"p.Arg625Gln","c.1874G>A","MODERATE","625/686",12,{"$nulls":5},"5","265","208","204","157","242","194","0","0","0","0.4021",{"$nulls":20},"1.8473410000000001","4.46","0.73","0.998602","-0.78","0.432","0.245","0.231",{"$nulls":3},"ESP6500_AA_AF",0.01929187471629596,{"$nulls":7},"0/0","263,0","0","263","0/1","122,82","0.402","204",null,"chr9:70218559:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4013"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MAP3K7","chr6:90516533","MAP3K7(S597R)",null,null,"splice variant (In isoform 1C and isoform 1D. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Frontometaphyseal dysplasia 2 (FMD2) [MIM:617137]: A form of frontometaphyseal dysplasia, a progressive sclerosing skeletal dysplasia affecting the long bones and skull. Characteristic features include supraorbital hyperostosis, cranial hyperostosis, undermodeling of the small bones, flared metaphyses, and digital anomalies. Extra-skeletal manifestations include hearing loss, cardiac malformations, and stenosis, particularly of the upper airway and urinary tract. FMD2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27426733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiospondylocarpofacial syndrome (CSCF) [MIM:157800]: A syndrome characterized by growth retardation, dysmorphic facial features, brachydactyly with carpal-tarsal fusion and extensive posterior cervical vertebral synostosis, cardiac septal defects with valve dysplasia, and deafness with inner ear malformations. CSCF transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27426734}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. Plays an important role in the cascades of cellular responses evoked by changes in the environment. Mediates signal transduction of TRAF6, various cytokines including interleukin-1 (IL-1), transforming growth factor-beta (TGFB), TGFB-related factors like BMP2 and BMP4, toll-like receptors (TLR), tumor necrosis factor receptor CD40 and B-cell receptor (BCR). Ceramides are also able to activate MAP3K7/TAK1. Once activated, acts as an upstream activator of the MKK/JNK signal transduction cascade and the p38 MAPK signal transduction cascade through the phosphorylation and activation of several MAP kinase kinases like MAP2K1/MEK1, MAP2K3/MKK3, MAP2K6/MKK6 and MAP2K7/MKK7. These MAP2Ks in turn activate p38 MAPKs, c-jun N-terminal kinases (JNKs) and I-kappa-B kinase complex (IKK). Both p38 MAPK and JNK pathways control the transcription factors activator protein-1 (AP-1), while nuclear factor-kappa B is activated by IKK. MAP3K7 activates also IKBKB and MAPK8/JNK1 in response to TRAF6 signaling and mediates BMP2- induced apoptosis. In osmotic stress signaling, plays a major role in the activation of MAPK8/JNK1, but not that of NF-kappa-B. Promotes TRIM5 capsid-specific restriction activity. {ECO:0000269|PubMed:10094049, ECO:0000269|PubMed:11460167, ECO:0000269|PubMed:12589052, ECO:0000269|PubMed:16845370, ECO:0000269|PubMed:16893890, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:8663074, ECO:0000269|PubMed:9079627}.; ","level2",{"$nulls":3},"p.Ser597Arg","c.1789A>C","MODERATE","597/606",17,{"$nulls":5},"4","175","289",null,null,"139","224","0","0","0","0.1116",{"$nulls":20},"2.543232","-0.93;-0.93;.",".;0.345;.","0.975791;0.975791;0.988656;1;1","-0.66;-0.65;-1.47","0.062;0.037;.","0.098;0.042;0.516","0.235;0.215;0.348",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK,kWNT",null,null,"C2931461| C4310697","0/0","174,0","0","174","0/1","259,28","0.0976","287",null,"chr6:90516533:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MAP3K7","chr6:90516533","MAP3K7(S597R)",null,null,"splice variant (In isoform 1C and isoform 1D. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Frontometaphyseal dysplasia 2 (FMD2) [MIM:617137]: A form of frontometaphyseal dysplasia, a progressive sclerosing skeletal dysplasia affecting the long bones and skull. Characteristic features include supraorbital hyperostosis, cranial hyperostosis, undermodeling of the small bones, flared metaphyses, and digital anomalies. Extra-skeletal manifestations include hearing loss, cardiac malformations, and stenosis, particularly of the upper airway and urinary tract. FMD2 inheritance is autosomal dominant. {ECO:0000269|PubMed:27426733}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiospondylocarpofacial syndrome (CSCF) [MIM:157800]: A syndrome characterized by growth retardation, dysmorphic facial features, brachydactyly with carpal-tarsal fusion and extensive posterior cervical vertebral synostosis, cardiac septal defects with valve dysplasia, and deafness with inner ear malformations. CSCF transmission pattern is consistent with autosomal dominant inheritance. {ECO:0000269|PubMed:27426734}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Serine/threonine kinase which acts as an essential component of the MAP kinase signal transduction pathway. Plays an important role in the cascades of cellular responses evoked by changes in the environment. Mediates signal transduction of TRAF6, various cytokines including interleukin-1 (IL-1), transforming growth factor-beta (TGFB), TGFB-related factors like BMP2 and BMP4, toll-like receptors (TLR), tumor necrosis factor receptor CD40 and B-cell receptor (BCR). Ceramides are also able to activate MAP3K7/TAK1. Once activated, acts as an upstream activator of the MKK/JNK signal transduction cascade and the p38 MAPK signal transduction cascade through the phosphorylation and activation of several MAP kinase kinases like MAP2K1/MEK1, MAP2K3/MKK3, MAP2K6/MKK6 and MAP2K7/MKK7. These MAP2Ks in turn activate p38 MAPKs, c-jun N-terminal kinases (JNKs) and I-kappa-B kinase complex (IKK). Both p38 MAPK and JNK pathways control the transcription factors activator protein-1 (AP-1), while nuclear factor-kappa B is activated by IKK. MAP3K7 activates also IKBKB and MAPK8/JNK1 in response to TRAF6 signaling and mediates BMP2- induced apoptosis. In osmotic stress signaling, plays a major role in the activation of MAPK8/JNK1, but not that of NF-kappa-B. Promotes TRIM5 capsid-specific restriction activity. {ECO:0000269|PubMed:10094049, ECO:0000269|PubMed:11460167, ECO:0000269|PubMed:12589052, ECO:0000269|PubMed:16845370, ECO:0000269|PubMed:16893890, ECO:0000269|PubMed:21512573, ECO:0000269|PubMed:8663074, ECO:0000269|PubMed:9079627}.; ","level2",{"$nulls":3},"p.Ser597Arg","c.1789A>C","MODERATE","597/606",17,{"$nulls":5},"4","175","197","159","182","139","154","0","0","0","0.1558",{"$nulls":20},"2.543232","-0.93;-0.93;.",".;0.345;.","0.975791;0.975791;0.988656;1;1","-0.66;-0.65;-1.47","0.062;0.037;.","0.098;0.042;0.516","0.235;0.215;0.348",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK,kWNT",null,null,"C2931461| C4310697","0/0","174,0","0","174","0/1","164,29","0.1503","193",null,"chr6:90516533:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1538"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MAST2","chr1:46029875","MAST2(D789H)",null,null,"domain (AGC-kinase C-terminal )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Appears to link the dystrophin/utrophin network with microtubule filaments via the syntrophins. Phosphorylation of DMD or UTRN may modulate their affinities for associated proteins. Functions in a multi-protein complex in spermatid maturation. Regulates lipopolysaccharide-induced IL-12 synthesis in macrophages by forming a complex with TRAF6, resulting in the inhibition of TRAF6 NF-kappa-B activation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp789His","c.2365G>C","MODERATE","789/1798",20,{"$nulls":5},"5","532","569","415","414","418","473","0","0","0","0.1797",{"$nulls":20},"4.035772","1.8;1.8;.","3.165;.;.","1","-6.72;-6.76;.","1.0;.;.","0.005;0.012;.","0.811;.;0.915",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","522,0","0","522","0/1","460,83","0.1529","543",null,"chr1:46029875:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.157"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MBOAT4","chr8:30144567","MBOAT4(I12K)",null,null,"transmembrane region (Helical ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the octanoylation of ghrelin at 'Ser-3'. Can use a variety of fatty acids as substrates including octanoic acid, decanoic acid and tetradecanoic acid. {ECO:0000269|PubMed:18443287}.; ",{"$nulls":4},"p.Ile12Lys","c.35T>A","MODERATE","12/435",1,{"$nulls":5},"3",{"$nulls":4},"188","123",null,null,"0","0.561",{"$nulls":20},"2.228333","1.93",null,"1","-1.96","0.037","0.025","0.421",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","201,0","0","206","0/1","62,7","0.1014","143",null,"chr8:30144567:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MBOAT4","chr8:30144568","MBOAT4(H10fs)",null,null,"transmembrane region (Helical ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Mediates the octanoylation of ghrelin at 'Ser-3'. Can use a variety of fatty acids as substrates including octanoic acid, decanoic acid and tetradecanoic acid. {ECO:0000269|PubMed:18443287}.; ",{"$nulls":4},"p.His10fs","c.30_33delTCCT","HIGH","10/435",1,{"$nulls":5},"3",{"$nulls":4},"162","143",null,null,"0","0.0979",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","190,0","0","204","0/1","148,19","0.1138","186",null,"chr8:30144568:TAGGA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MBOAT4","chr8:30144568","MBOAT4(H10fs)",null,null,"transmembrane region (Helical ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Mediates the octanoylation of ghrelin at 'Ser-3'. Can use a variety of fatty acids as substrates including octanoic acid, decanoic acid and tetradecanoic acid. {ECO:0000269|PubMed:18443287}.; ",{"$nulls":4},"p.His10fs","c.30_33delTCCT","HIGH","10/435",1,{"$nulls":5},"3",{"$nulls":4},"162","120",null,null,"0","0.5417",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","190,0","0","204","0/1","56,64","0.5333","142",null,"chr8:30144568:TAGGA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MBTPS2","chrX:21853498","MBTPS2(C222Y)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Olmsted syndrome, X-linked (OLMSX) [MIM:300918]: A rare congenital disorder characterized by bilateral mutilating palmoplantar keratoderma and periorificial keratotic plaques with severe itching at all lesions. Diffuse alopecia, constriction of digits, and onychodystrophy have also been reported. Infections and squamous cell carcinomas can arise on the keratotic areas. The digital constriction may progress to autoamputation of fingers and toes. {ECO:0000269|PubMed:22931912}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratosis follicularis spinulosa decalvans X-linked (KFSDX) [MIM:308800]: A rare disorder affecting the skin and the eye. Affected men show thickening of the skin of the neck, ears, and extremities, especially the palms and soles, loss of eyebrows, eyelashes and beard, thickening of the eyelids with blepharitis and ectropion, and corneal degeneration. {ECO:0000269|PubMed:20672378}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Intramembrane proteolysis of sterol-regulatory element- binding proteins (SREBPs) within the first transmembrane segment thereby releasing the N-terminal segment with a portion of the transmembrane segment attached. Site-2 cleavage comes after site-1 cleavage which takes place in the lumenal loop.; ",{"$nulls":4},"p.Cys222Tyr","c.665G>A","MODERATE","222/519",5,{"$nulls":5},"5","218","363","142","226","208","332","0","0","0","0.0813",{"$nulls":20},"3.942844","-3.0","2.69;.","1","-9.49;-9.46","0.995;0.99","0.0","0.889;0.881",{"$nulls":3},"Unknown",-1,"XL","Keratosis follicularis spinulosa decalvans, X-linked; IFAP syndrome with or without BRESHECK syndrome; Palmoplantar keratoderma, mutilating, with periorificial keratotic plaques, X-linked","Craniofacial; Dermatologic; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C1839988| C3806745| C4746956| C3887525","0/0","217,0","0","217","0/1","319,34","0.0963","353",null,"chrX:21853498:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1018"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MBTPS2","chrX:21853498","MBTPS2(C222Y)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Olmsted syndrome, X-linked (OLMSX) [MIM:300918]: A rare congenital disorder characterized by bilateral mutilating palmoplantar keratoderma and periorificial keratotic plaques with severe itching at all lesions. Diffuse alopecia, constriction of digits, and onychodystrophy have also been reported. Infections and squamous cell carcinomas can arise on the keratotic areas. The digital constriction may progress to autoamputation of fingers and toes. {ECO:0000269|PubMed:22931912}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratosis follicularis spinulosa decalvans X-linked (KFSDX) [MIM:308800]: A rare disorder affecting the skin and the eye. Affected men show thickening of the skin of the neck, ears, and extremities, especially the palms and soles, loss of eyebrows, eyelashes and beard, thickening of the eyelids with blepharitis and ectropion, and corneal degeneration. {ECO:0000269|PubMed:20672378}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Intramembrane proteolysis of sterol-regulatory element- binding proteins (SREBPs) within the first transmembrane segment thereby releasing the N-terminal segment with a portion of the transmembrane segment attached. Site-2 cleavage comes after site-1 cleavage which takes place in the lumenal loop.; ",{"$nulls":4},"p.Cys222Tyr","c.665G>A","MODERATE","222/519",5,{"$nulls":5},"5","218","233","142","141","207","219","0","0","0","0.1598",{"$nulls":20},"3.942844","-3.0","2.69;.","1","-9.49;-9.46","0.995;0.99","0.0","0.889;0.881",{"$nulls":3},"Unknown",-1,"XL","Keratosis follicularis spinulosa decalvans, X-linked; IFAP syndrome with or without BRESHECK syndrome; Palmoplantar keratoderma, mutilating, with periorificial keratotic plaques, X-linked","Craniofacial; Dermatologic; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C1839988| C3806745| C4746956| C3887525","0/0","214,0","0","214","0/1","185,35","0.1591","220",null,"chrX:21853498:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1631"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MED12L","chr3:151190884","MED12L(E641*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May be a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu641*","c.1921G>T","HIGH","641/2145",13,{"$nulls":5},"4","381","590","263","381","361","534","0.0026","0.0026","0","0.2341",{"$nulls":5},"(MED12L|ENSG00000144893|1|1.00)","(MED12L|ENSG00000144893|1|1.00)",{"$nulls":13},"7.914207",null,null,"1",{"$nulls":3},"0.396;0.392;0.481;0.475",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN280885","0/0","370,1","0.0027","371","0/1","420,151","0.2644","571",null,"chr3:151190884:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2546"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MED12L","chr3:151190884","MED12L(E641*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May be a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu641*","c.1921G>T","HIGH","641/2145",13,{"$nulls":5},"4","381","449","263","287","361","422","0.0026","0.0026","0","0.2701",{"$nulls":5},"(MED12L|ENSG00000144893|1|1.00)","(MED12L|ENSG00000144893|1|1.00)",{"$nulls":13},"7.914207",null,null,"1",{"$nulls":3},"0.396;0.392;0.481;0.475",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN280885","0/0","373,1","0.0027","374","0/1","319,123","0.2783","442",null,"chr3:151190884:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2822"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MRGPRG","chr11:3217981","MRGPRG(G278D)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Orphan receptor. May regulate nociceptor function and/or development, including the sensation or modulation of pain (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Gly278Asp","c.833G>A","MODERATE","278/289",1,{"$nulls":5},"5","437","203","313","148","391","175","0","0","0","0.0571",{"$nulls":20},"0.271727","4.02","1.34","1","-1.6",null,"0.181","0.102",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","427,0","0","427","0/1","185,13","0.0657","198",null,"chr11:3217981:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0541"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MRM1","chr17:36608261","MRM1(I303T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O- methylguanosine at position 1145 (Gm1145) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a universally conserved modification in the peptidyl transferase domain of the mtLSU rRNA. {ECO:0000269|PubMed:25074936}.; ","mitocarta",{"$nulls":3},"p.Ile303Thr","c.908T>C","MODERATE","303/353",5,{"$nulls":5},"5","355","412","292","314","284","357","0","0","0","0.3305",{"$nulls":20},"4.111355",null,"2.125;.","0.999586",null,"0.94;.",null,"0.772;0.761",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","346,0","0","346","0/1","274,123","0.3098","397",null,"chr17:36608261:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.328"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MRM1","chr17:36608261","MRM1(I303T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O- methylguanosine at position 1145 (Gm1145) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a universally conserved modification in the peptidyl transferase domain of the mtLSU rRNA. {ECO:0000269|PubMed:25074936}.; ","mitocarta",{"$nulls":3},"p.Ile303Thr","c.908T>C","MODERATE","303/353",5,{"$nulls":5},"5","355","194","292","157","284","170","0","0","0","0.7353",{"$nulls":20},"4.111355",null,"2.125;.","0.999586",null,"0.94;.",null,"0.772;0.761",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","346,0","0","346","0/1","55,134","0.709","189",null,"chr17:36608261:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7134"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MTHFD1L","chr6:151015580","MTHFD1L(A826S)",null,null,"region of interest (Formyltetrahydrofolate synthetase ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May provide the missing metabolic reaction required to link the mitochondria and the cytoplasm in the mammalian model of one-carbon folate metabolism in embryonic an transformed cells complementing thus the enzymatic activities of MTHFD2. {ECO:0000250, ECO:0000269|PubMed:16171773}.; ","mitocarta",{"$nulls":3},"p.Ala826Ser","c.2476G>T","MODERATE","826/979",24,{"$nulls":5},"5","603","690","459","509","521","588","0","0","0","0.1054",{"$nulls":20},"4.236114","1.87;.;.;1.87","2.805;.;.;.","1","-2.87;.;.;-2.99","1.0;0.999;.;.","0.006;.;.;0.012","0.739;0.754;0.731;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","597,0","0","597","0/1","587,72","0.1093","659",null,"chr6:151015580:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1081"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MTHFD1L","chr6:151015580","MTHFD1L(A826S)",null,null,"region of interest (Formyltetrahydrofolate synthetase ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May provide the missing metabolic reaction required to link the mitochondria and the cytoplasm in the mammalian model of one-carbon folate metabolism in embryonic an transformed cells complementing thus the enzymatic activities of MTHFD2. {ECO:0000250, ECO:0000269|PubMed:16171773}.; ","mitocarta",{"$nulls":3},"p.Ala826Ser","c.2476G>T","MODERATE","826/979",24,{"$nulls":5},"5","603","350","459","271","523","305","0","0","0","0.282",{"$nulls":20},"4.236114","1.87;.;.;1.87","2.805;.;.;.","1","-2.87;.;.;-2.99","1.0;0.999;.;.","0.006;.;.;0.012","0.739;0.754;0.731;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","597,0","0","597","0/1","239,90","0.2736","329",null,"chr6:151015580:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2546"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MTUS2","chr13:29026890","MTUS2(K741T)",null,null,"region of interest (Mediates interaction with MAPRE1 ), splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds microtubules. Together with MAPRE1 may target the microtubule depolymerase KIF2C to the plus-end of microtubules. May regulate the dynamics of microtubules at their growing distal tip. {ECO:0000269|PubMed:19543227}.; ",{"$nulls":4},"p.Lys741Thr","c.2222A>C","MODERATE","741/1379",3,2,{"$nulls":4},"5","360","173","260","121","324","150","0","0","0","0.2733",{"$nulls":20},"3.9933490000000003",null,null,"0.941121",{"$nulls":3},"0.673",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","351,0","0","351","0/1","119,51","0.3","170",null,"chr13:29026890:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2727"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MUC22","chr6:31026836","MUC22(A469T)",null,null,"topological domain (Extracellular ), region of interest (124 X 10 AA approximate repeats ), compositionally biased region (Thr-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala469Thr","c.1405G>A","MODERATE","469/1773",2,{"$nulls":5},"4","1138","1218","903","914","679","704","0","0","0","0.0739",{"$nulls":20},"-0.375364","2.22","0.345","1","-0.25",null,"1.0","0.041",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1107,0","0","1107","0/1","1052,89","0.078","1141",null,"chr6:31026836:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0711"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","MUC6","chr11:1018179","MUC6(S1541Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May provide a mechanism for modulation of the composition of the protective mucus layer related to acid secretion or the presence of bacteria and noxious agents in the lumen. Plays an important role in the cytoprotection of epithelial surfaces and are used as tumor markers in a variety of cancers. May play a role in epithelial organogenesis. {ECO:0000269|PubMed:10209489, ECO:0000269|PubMed:10330458, ECO:0000269|PubMed:11988092}.; ",{"$nulls":4},"p.Ser1541Tyr","c.4622C>A","MODERATE","1541/2439",31,{"$nulls":5},"3",null,null,"473","398","368","287",null,null,"0","0.3519",{"$nulls":20},"0.862075","2.17","2.085","1","-1.46","0.001","0.008","0.085",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","572,0","0","611","0/1","316,136","0.3009","506",null,"chr11:1018179:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2714"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","MUC6","chr11:1018179","MUC6(S1541Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May provide a mechanism for modulation of the composition of the protective mucus layer related to acid secretion or the presence of bacteria and noxious agents in the lumen. Plays an important role in the cytoprotection of epithelial surfaces and are used as tumor markers in a variety of cancers. May play a role in epithelial organogenesis. {ECO:0000269|PubMed:10209489, ECO:0000269|PubMed:10330458, ECO:0000269|PubMed:11988092}.; ",{"$nulls":4},"p.Ser1541Tyr","c.4622C>A","MODERATE","1541/2439",31,{"$nulls":5},"3",null,null,"473","247","368","202",null,null,"0","0.6634",{"$nulls":20},"0.862075","2.17","2.085","1","-1.46","0.001","0.008","0.085",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","572,0","0","611","0/1","125,160","0.5614","317",null,"chr11:1018179:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5425"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","NCKAP1","chr2:182925745","NCKAP1(A1121V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Part of the WAVE complex that regulates lamellipodia formation. The WAVE complex regulates actin filament reorganization via its interaction with the Arp2/3 complex. Actin remodeling activity is regulated by RAC1. As component of the WAVE1 complex, required for BDNF-NTRK2 endocytic trafficking and signaling from early endosomes. {ECO:0000250|UniProtKB:P28660}.; ",{"$nulls":4},"p.Ala1121Val","c.3362C>T","MODERATE","1121/1134",32,{"$nulls":5},"5","127","165","94","118","96","122","0","0","0","0.082",{"$nulls":20},"4.251256","1.35","1.61;.","1","-3.59","1.0","0.001","0.792;0.784",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","124,0","0","124","0/1","150,11","0.0683","161",null,"chr2:182925745:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0763"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NCKAP1","chr2:182925745","NCKAP1(A1121V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Part of the WAVE complex that regulates lamellipodia formation. The WAVE complex regulates actin filament reorganization via its interaction with the Arp2/3 complex. Actin remodeling activity is regulated by RAC1. As component of the WAVE1 complex, required for BDNF-NTRK2 endocytic trafficking and signaling from early endosomes. {ECO:0000250|UniProtKB:P28660}.; ",{"$nulls":4},"p.Ala1121Val","c.3362C>T","MODERATE","1121/1134",32,{"$nulls":5},"5","127","83","94","61","95","68","0","0","0","0.2353",{"$nulls":20},"4.251256","1.35","1.61;.","1","-3.59","1.0","0.001","0.792;0.784",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","124,0","0","124","0/1","64,19","0.2289","83",null,"chr2:182925745:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2131"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","NCKAP5L","chr12:49803981","NCKAP5L(D22Y)",null,null,"region of interest (Mediates interaction with CDK5RAP2 and is required for homodimerization and microtubule bundle formation )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulates microtubule organization and stabilization. Promotes microtubule growth and bundling formation and stabilizes microtubules by increasing intense acetylation of microtubules (PubMed:26482847, PubMed:26485573). Both tubulin-binding and homodimer formation are required for NCKAP5L-mediated microtubule bundle formation (PubMed:26485573). {ECO:0000269|PubMed:26482847, ECO:0000269|PubMed:26485573}.; ",{"$nulls":4},"p.Asp22Tyr","c.64G>T","MODERATE","22/1334",3,{"$nulls":5},"5","207","214","155","147","160","165","0","0","0","0.097",{"$nulls":20},"3.20421","0.8",null,"0.999998","-1.6",null,"0.002","0.333",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","195,0","0","195","0/1","175,18","0.0933","193",null,"chr12:49803981:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0952"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","NDUFAF5","chr20:13785106","NDUFAF5(R13Q)",null,null,"transit peptide (Mitochondrion )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Mitochondrial complex I deficiency (MT-C1D) [MIM:252010]: A disorder of the mitochondrial respiratory chain that causes a wide range of clinical manifestations from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. {ECO:0000269|PubMed:18940309}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leigh syndrome (LS) [MIM:256000]: An early-onset progressive neurodegenerative disorder characterized by the presence of focal, bilateral lesions in one or more areas of the central nervous system including the brainstem, thalamus, basal ganglia, cerebellum and spinal cord. Clinical features depend on which areas of the central nervous system are involved and include subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, and dysphagia. {ECO:0000269|PubMed:19542079, ECO:0000269|PubMed:21607760}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Arginine hydroxylase involved in the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I, MT-ND1) at early stages (PubMed:18940309, PubMed:27226634). Acts by mediating hydroxylation of 'Arg-111' of NDUFS7 (PubMed:27226634). May also have methyltransferase activity (Probable). {ECO:0000269|PubMed:18940309, ECO:0000269|PubMed:27226634, ECO:0000305}.; ",{"$nulls":4},"p.Arg13Gln","c.38G>A","MODERATE","13/345",1,{"$nulls":5},"5","194","298","166","266","136","215","0","0","0","0.1488",{"$nulls":20},"0.891294","-1.57;-1.34","1.79","1","-0.6;-0.67","0.741;0.832","0.028;0.023","0.352;0.236",{"$nulls":3},"Unknown",-1,"AR","Mitochondrial complex I deficiency","Biochemical; Cardiovascular; Gastrointestinal; Neurologic; Ophthalmologic",{"$nulls":3},"C4748785","0/0","191,0","0","191","0/1","247,37","0.1303","284",null,"chr20:13785106:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1165"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NEB","chr2:151643987","NEB(W2596L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: This giant muscle protein may be involved in maintaining the structural integrity of sarcomeres and the membrane system associated with the myofibrils. Binds and stabilize F-actin.; ",{"$nulls":4},"p.Trp2596Leu","c.7787G>T","MODERATE","2596/8560",57,{"$nulls":5},"4","1576","883","1252","692","1342","258","0","0","0","0.3023",{"$nulls":20},"2.33618","0.97;0.97;.;0.97;0.97;0.97;0.97","2.3;2.3;.;2.3;2.3;2.3;2.3","0.955031;0.99695;0.99695;0.955031","-3.25;-3.44;.;-3.44;-3.25;.;.",".;.;.;.;0.482;.;.","0.09;0.293;.;0.279;0.09;.;.","0.495;0.579;0.577;0.579;0.501;0.579;0.579",{"$nulls":3},"Unknown",-1,"AR","Nemaline myopathy 2","Musculoskeletal",null,"This gene encodes nebulin, a giant protein component of the cytoskeletal matrix that coexists with the thick and thin filaments within the sarcomeres of skeletal muscle. In most vertebrates, nebulin accounts for 3 to 4% of the total myofibrillar protein. The encoded protein contains approximately 30-amino acid long modules that can be classified into 7 types and other repeated modules. Protein isoform sizes vary from 600 to 800 kD due to alternative splicing that is tissue-, species-,and developmental stage-specific. Of the 183 exons in the nebulin gene, at least 43 are alternatively spliced, although exons 143 and 144 are not found in the same transcript. Of the several thousand transcript variants predicted for nebulin, the RefSeq Project has decided to create three representative RefSeq records. Mutations in this gene are associated with recessive nemaline myopathy. [provided by RefSeq, Sep 2009].",null,"C1850569","0/0","1543,0","0","1543","0/1","552,288","0.3429","840",null,"chr2:151643987:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3382"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","NEDD4","chr15:55874008","NEDD4(T517S)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Specifically ubiquitinates 'Lys-63' in target proteins (PubMed:23644597). Involved in the pathway leading to the degradation of VEGFR-2/KDFR, independently of its ubiquitin-ligase activity. Monoubiquitinates IGF1R at multiple sites, thus leading to receptor internalization and degradation in lysosomes. Ubiquitinates FGFR1, leading to receptor internalization and degradation in lysosomes. Promotes ubiquitination of RAPGEF2. According to PubMed:18562292 the direct link between NEDD4 and PTEN regulation through polyubiquitination described in PubMed:17218260 is questionable. Involved in ubiquitination of ERBB4 intracellular domain E4ICD. Involved in the budding of many viruses. Part of a signaling complex composed of NEDD4, RAP2A and TNIK which regulates neuronal dendrite extension and arborization during development. Ubiquitinates TNK2 and regulates EGF-induced degradation of EGFR and TNF2. Ubiquitinates BRAT1 and this ubiquitination is enhanced in the presence of NDFIP1 (PubMed:25631046). {ECO:0000269|PubMed:11598133, ECO:0000269|PubMed:17218260, ECO:0000269|PubMed:18305167, ECO:0000269|PubMed:18562292, ECO:0000269|PubMed:20086093, ECO:0000269|PubMed:21399620, ECO:0000269|PubMed:21765395, ECO:0000269|PubMed:23644597, ECO:0000269|PubMed:25631046}.; ",{"$nulls":4},"p.Thr517Ser","c.1549A>T","MODERATE","517/1319",2,{"$nulls":5},"5","60","104","38","57","54","86","0","0","0","0.3023",{"$nulls":20},"4.447375","-0.51;-0.29;-0.51","2.255;.;2.255","1","-3.39;-3.33;-3.51","0.942;0.993;0.996","0.103;0.005;0.247","0.622;0.468;0.513",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","59,0","0","59","0/1","64,32","0.3333","96",null,"chr15:55874008:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3158"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NEDD4","chr15:55874008","NEDD4(T517S)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Specifically ubiquitinates 'Lys-63' in target proteins (PubMed:23644597). Involved in the pathway leading to the degradation of VEGFR-2/KDFR, independently of its ubiquitin-ligase activity. Monoubiquitinates IGF1R at multiple sites, thus leading to receptor internalization and degradation in lysosomes. Ubiquitinates FGFR1, leading to receptor internalization and degradation in lysosomes. Promotes ubiquitination of RAPGEF2. According to PubMed:18562292 the direct link between NEDD4 and PTEN regulation through polyubiquitination described in PubMed:17218260 is questionable. Involved in ubiquitination of ERBB4 intracellular domain E4ICD. Involved in the budding of many viruses. Part of a signaling complex composed of NEDD4, RAP2A and TNIK which regulates neuronal dendrite extension and arborization during development. Ubiquitinates TNK2 and regulates EGF-induced degradation of EGFR and TNF2. Ubiquitinates BRAT1 and this ubiquitination is enhanced in the presence of NDFIP1 (PubMed:25631046). {ECO:0000269|PubMed:11598133, ECO:0000269|PubMed:17218260, ECO:0000269|PubMed:18305167, ECO:0000269|PubMed:18562292, ECO:0000269|PubMed:20086093, ECO:0000269|PubMed:21399620, ECO:0000269|PubMed:21765395, ECO:0000269|PubMed:23644597, ECO:0000269|PubMed:25631046}.; ",{"$nulls":4},"p.Thr517Ser","c.1549A>T","MODERATE","517/1319",2,{"$nulls":5},"5","60","37","38","22","53","35","0","0","0","0.5714",{"$nulls":20},"4.447375","-0.51;-0.29;-0.51","2.255;.;2.255","1","-3.39;-3.33;-3.51","0.942;0.993;0.996","0.103;0.005;0.247","0.622;0.468;0.513",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","59,0","0","59","0/1","17,19","0.5278","36",null,"chr15:55874008:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5455"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","NKX6-3","chr8:41650453","NKX6-3(T14A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative transcription factor, which may be involved in patterning of central nervous system and pancreas. {ECO:0000250}.; ",{"$nulls":4},"p.Thr14Ala","c.40A>G","MODERATE","14/265",1,{"$nulls":5},"5","473","566","335","397","419","506","0","0","0","0.1502",{"$nulls":20},"1.604236","-2.79","0.09","0.912918","0.22",null,"0.503","0.079",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The NKX family of homeodomain proteins controls numerous developmental processes. Members of the NKX6 subfamily, including NKX6-3, are involved in development of the central nervous system (CNS), gastrointestinal tract, and pancreas (Alanentalo et al., 2006 [PubMed 16326147]).[supplied by OMIM, Mar 2008].  ",null,null,"0/0","465,0","0","465","0/1","452,80","0.1504","532",null,"chr8:41650453:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1486"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NKX6-3","chr8:41650453","NKX6-3(T14A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Putative transcription factor, which may be involved in patterning of central nervous system and pancreas. {ECO:0000250}.; ",{"$nulls":4},"p.Thr14Ala","c.40A>G","MODERATE","14/265",1,{"$nulls":5},"5","473","369","335","267","418","324","0","0","0","0.4846",{"$nulls":20},"1.604236","-2.79","0.09","0.912918","0.22",null,"0.503","0.079",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The NKX family of homeodomain proteins controls numerous developmental processes. Members of the NKX6 subfamily, including NKX6-3, are involved in development of the central nervous system (CNS), gastrointestinal tract, and pancreas (Alanentalo et al., 2006 [PubMed 16326147]).[supplied by OMIM, Mar 2008].  ",null,null,"0/0","465,0","0","465","0/1","183,166","0.4756","349",null,"chr8:41650453:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4757"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NPBWR1","chr8:52940065","NPBWR1(A53V)",null,null,"transmembrane region (Helical; Name=1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Interacts specifically with a number of opioid ligands. Receptor for neuropeptides B and W, which may be involved in neuroendocrine system regulation, food intake and the organization of other signals. Has a higher affinity for neuropeptide B.; ",{"$nulls":4},"p.Ala53Val","c.158C>T","MODERATE","53/328",1,{"$nulls":5},"3","636","364",{"$nulls":4},"0.0016","0.0016",{"$nulls":22},"1.7682959999999999","1.37","0.345","0.674998","0.06","0.008","0.57","0.036",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","625,1","0.0016","626","0/1","331,22","0.0623","353",null,"chr8:52940065:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","NRP2","chr2:205763703","NRP2(D692H)",null,null,"topological domain (Extracellular ), domain (MAM ), splice variant (In isoform s9. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF.; ",{"$nulls":4},"p.Asp692His","c.2074G>C","MODERATE","692/931",13,{"$nulls":5},"5","727","1108","556","812","563","868","0","0","0","0.2293",{"$nulls":20},"3.401925","4.41","1.73","1","-1.96","0.655;0.582;0.582;0.582;0.582","0.003;0.004;0.003;0.004;0.003","0.315;0.357;0.352;0.313;0.352",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","701,0","0","701","0/1","826,233","0.22","1059",null,"chr2:205763703:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2204"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NRP2","chr2:205763703","NRP2(D692H)",null,null,"topological domain (Extracellular ), domain (MAM ), splice variant (In isoform s9. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF.; ",{"$nulls":4},"p.Asp692His","c.2074G>C","MODERATE","692/931",13,{"$nulls":5},"5","727","595","556","448","560","489","0","0","0","0.2331",{"$nulls":20},"3.401925","4.41","1.73","1","-1.96","0.655;0.582;0.582;0.582;0.582","0.003;0.004;0.003;0.004;0.003","0.315;0.357;0.352;0.313;0.352",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","706,0","0","706","0/1","445,121","0.2138","566",null,"chr2:205763703:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2299"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","NT5DC3","chr12:103806368","NT5DC3(M160V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Met160Val","c.478A>G","MODERATE","160/548",4,{"$nulls":5},"3",null,null,"408","202",{"$nulls":26},"3.206578","2.03","2.255","0.999997","-2.86","0.771","0.18","0.876",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","562,0","0","563","0/1","284,15","0.0502","299",null,"chr12:103806368:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0594"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","OBSCN","chr1:228298511","OBSCN(T4335I)",null,null,"domain (Ig-like 44 ), splice variant (In isoform 4. ), strand ",{"$nulls":3},255,"PASS","Missense","rs892193568",-1,"DISEASE: Note=A chromosomal aberration involving OBSCN has been found in Wilms tumor. Translocation t(1;7)(q42;p15) with PTHB1. {ECO:0000269|PubMed:12618763}.; ","FUNCTION: Structural component of striated muscles which plays a role in myofibrillogenesis. Probably involved in the assembly of myosin into sarcomeric A bands in striated muscle (PubMed:11448995, PubMed:16205939). Has serine/threonine protein kinase activity and phosphorylates N-cadherin CDH2 and sodium/potassium-transporting ATPase subunit ATP1B1 (By similarity). {ECO:0000250|UniProtKB:A2AAJ9, ECO:0000269|PubMed:11448995, ECO:0000269|PubMed:16205939}.; ",{"$nulls":4},"p.Thr4335Ile","c.13004C>T","MODERATE","4335/8923",48,{"$nulls":5},"5","537","620","448","484","448","525","0","0","0","0.059",{"$nulls":20},"0.458082","1.47;1.15",null,"1",".;-0.61",null,".;0.678","0.226",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The obscurin gene spans more than 150 kb, contains over 80 exons and encodes a protein of approximately 720 kDa. The encoded protein contains 68 Ig domains, 2 fibronectin domains, 1 calcium/calmodulin-binding domain, 1 RhoGEF domain with an associated PH domain, and 2 serine-threonine kinase domains. This protein belongs to the family of giant sacromeric signaling proteins that includes titin and nebulin, and may have a role in the organization of myofibrils during assembly and may mediate interactions between the sarcoplasmic reticulum and myofibrils. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008].",null,null,"0/0","535,0","0","535","0/1","551,37","0.0629","588",null,"chr1:228298511:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0579"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","OR4Q3","chr14:19747474","OR4Q3(G16D)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs1193790122",-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Gly16Asp","c.47G>A","MODERATE","16/313",1,{"$nulls":5},"5","705","638","534","470","633","566","0","0","0","0.0901",{"$nulls":20},"3.5109909999999998",".;5.95",".;3.21","0.573052",".;-5.76",".;1.0",".;0.005",".;0.574",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","694,0","0","694","0/1","552,68","0.1097","620",null,"chr14:19747474:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1191"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","OR4Q3","chr14:19747474","OR4Q3(G16D)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs1193790122",-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Gly16Asp","c.47G>A","MODERATE","16/313",1,{"$nulls":5},"5","705","336","534","266","632","272","0","0","0","0.2022",{"$nulls":20},"3.5109909999999998",".;5.95",".;3.21","0.573052",".;-5.76",".;1.0",".;0.005",".;0.574",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","695,0","0","695","0/1","251,79","0.2394","330",null,"chr14:19747474:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2556"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","OR5T3","chr11:56253205","OR5T3(K336Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Lys336Gln","c.1006A>C","MODERATE","336/340",1,{"$nulls":5},"4","181","165",null,null,"170","148","0","0","0","0.1149",{"$nulls":20},"1.129904","1.15;.","1.125;.","1","-0.14;.","0.906;.","0.473;.","0.194;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","183,0","0","183","0/1","142,21","0.1288","163",null,"chr11:56253205:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","OR8A1","chr11:124570509","OR8A1(L148fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Leu148fs","c.442delC","HIGH","148/326",1,{"$nulls":5},"4","653","327","487","238","550","281","0.0016","0.0016","0","0.2669",{"$nulls":5},"(OR8A1|ENSG00000196119|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","625,0","0","625","0/1","230,81","0.2605","311",null,"chr11:124570509:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2857"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","OTUD7B","chr1:149959780","OTUD7B(T250R)",null,null,"domain (OTU ), region of interest (TRAF-binding ), region of interest (Catalytic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF- kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections (By similarity). Deubiquitinates ZAP70, and thereby regulates T cell receptor (TCR) signaling that leads to the activation of NF-kappa-B (PubMed:26903241). Plays a role in T cell homeostasis and is required for normal T cell responses, including production of IFNG and IL2 (By similarity). Mediates deubiquitination of EGFR (PubMed:22179831). Has deubiquitinating activity toward 'Lys-11', 'Lys-48' and 'Lys-63'-linked polyubiquitin chains (PubMed:27732584). Has a much higher catalytic rate with 'Lys-11'-linked polyubiquitin chains (in vitro); however the physiological significance of these data are unsure (PubMed:27732584). Hydrolyzes both linear and branched forms of polyubiquitin. {ECO:0000250|UniProtKB:B2RUR8, ECO:0000269|PubMed:11463333, ECO:0000269|PubMed:12682062, ECO:0000269|PubMed:18178551, ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:22179831, ECO:0000269|PubMed:23827681, ECO:0000269|PubMed:27732584}.; ",{"$nulls":4},"p.Thr250Arg","c.749C>G","MODERATE","250/843",7,{"$nulls":5},"5","597","665","421","448","558","608","0","0","0","0.1184",{"$nulls":20},"4.097092","1.57","1.61;.","1",".;-3.7","1.0;.",".;0.015","0.842;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","585,0","0","585","0/1","563,80","0.1244","643",null,"chr1:149959780:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1272"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","OTUD7B","chr1:149959780","OTUD7B(T250R)",null,null,"domain (OTU ), region of interest (TRAF-binding ), region of interest (Catalytic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF- kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections (By similarity). Deubiquitinates ZAP70, and thereby regulates T cell receptor (TCR) signaling that leads to the activation of NF-kappa-B (PubMed:26903241). Plays a role in T cell homeostasis and is required for normal T cell responses, including production of IFNG and IL2 (By similarity). Mediates deubiquitination of EGFR (PubMed:22179831). Has deubiquitinating activity toward 'Lys-11', 'Lys-48' and 'Lys-63'-linked polyubiquitin chains (PubMed:27732584). Has a much higher catalytic rate with 'Lys-11'-linked polyubiquitin chains (in vitro); however the physiological significance of these data are unsure (PubMed:27732584). Hydrolyzes both linear and branched forms of polyubiquitin. {ECO:0000250|UniProtKB:B2RUR8, ECO:0000269|PubMed:11463333, ECO:0000269|PubMed:12682062, ECO:0000269|PubMed:18178551, ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:22179831, ECO:0000269|PubMed:23827681, ECO:0000269|PubMed:27732584}.; ",{"$nulls":4},"p.Thr250Arg","c.749C>G","MODERATE","250/843",7,{"$nulls":5},"5","597","413","421","292","558","381","0","0","0","0.2625",{"$nulls":20},"4.097092","1.57","1.61;.","1",".;-3.7","1.0;.",".;0.015","0.842;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","585,0","0","585","0/1","293,110","0.273","403",null,"chr1:149959780:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2534"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","P4HB","chr17:81845957","P4HB(W364L)",null,null,"domain (Thioredoxin 2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cole-Carpenter syndrome 1 (CLCRP1) [MIM:112240]: A form of Cole-Carpenter syndrome, a disorder characterized by features of osteogenesis imperfecta such as bone deformities and severe bone fragility with frequent fractures, in association with craniosynostosis, ocular proptosis, hydrocephalus, growth failure and distinctive facial features. Craniofacial findings include marked frontal bossing, midface hypoplasia, and micrognathia. Despite the craniosynostosis and hydrocephalus, intellectual development is normal. CLCRP1 inheritance is autosomal dominant. {ECO:0000269|PubMed:25683117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: This multifunctional protein catalyzes the formation, breakage and rearrangement of disulfide bonds. At the cell surface, seems to act as a reductase that cleaves disulfide bonds of proteins attached to the cell. May therefore cause structural modifications of exofacial proteins. Inside the cell, seems to form/rearrange disulfide bonds of nascent proteins. At high concentrations, functions as a chaperone that inhibits aggregation of misfolded proteins. At low concentrations, facilitates aggregation (anti-chaperone activity). May be involved with other chaperones in the structural modification of the TG precursor in hormone biogenesis. Also acts a structural subunit of various enzymes such as prolyl 4-hydroxylase and microsomal triacylglycerol transfer protein MTTP. Receptor for LGALS9; the interaction retains P4HB at the cell surface of Th2 T helper cells, increasing disulfide reductase activity at the plasma membrane, altering the plasma membrane redox state and enhancing cell migration (PubMed:21670307). {ECO:0000269|PubMed:10636893, ECO:0000269|PubMed:12485997, ECO:0000269|PubMed:21670307}.; ",{"$nulls":4},"p.Trp364Leu","c.1091G>T","MODERATE","364/508",8,{"$nulls":5},"5","261","512","196","379","244","481","0","0","0","0.1393",{"$nulls":20},"4.288553","2.57","2.16;.","1","-12.3;.","1.0;.","0.001;.","0.694;0.664",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes the beta subunit of prolyl 4-hydroxylase, a highly abundant multifunctional enzyme that belongs to the protein disulfide isomerase family. When present as a tetramer consisting of two alpha and two beta subunits, this enzyme is involved in hydroxylation of prolyl residues in preprocollagen. This enzyme is also a disulfide isomerase containing two thioredoxin domains that catalyze the formation, breakage and rearrangement of disulfide bonds. Other known functions include its ability to act as a chaperone that inhibits aggregation of misfolded proteins in a concentration-dependent manner, its ability to bind thyroid hormone, its role in both the influx and efflux of S-nitrosothiol-bound nitric oxide, and its function as a subunit of the microsomal triglyceride transfer protein complex. [provided by RefSeq, Jul 2008].  ",null,"C4317154","0/0","258,0","0","258","0/1","427,71","0.1426","498",null,"chr17:81845957:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1398"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","P4HB","chr17:81845957","P4HB(W364L)",null,null,"domain (Thioredoxin 2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cole-Carpenter syndrome 1 (CLCRP1) [MIM:112240]: A form of Cole-Carpenter syndrome, a disorder characterized by features of osteogenesis imperfecta such as bone deformities and severe bone fragility with frequent fractures, in association with craniosynostosis, ocular proptosis, hydrocephalus, growth failure and distinctive facial features. Craniofacial findings include marked frontal bossing, midface hypoplasia, and micrognathia. Despite the craniosynostosis and hydrocephalus, intellectual development is normal. CLCRP1 inheritance is autosomal dominant. {ECO:0000269|PubMed:25683117}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: This multifunctional protein catalyzes the formation, breakage and rearrangement of disulfide bonds. At the cell surface, seems to act as a reductase that cleaves disulfide bonds of proteins attached to the cell. May therefore cause structural modifications of exofacial proteins. Inside the cell, seems to form/rearrange disulfide bonds of nascent proteins. At high concentrations, functions as a chaperone that inhibits aggregation of misfolded proteins. At low concentrations, facilitates aggregation (anti-chaperone activity). May be involved with other chaperones in the structural modification of the TG precursor in hormone biogenesis. Also acts a structural subunit of various enzymes such as prolyl 4-hydroxylase and microsomal triacylglycerol transfer protein MTTP. Receptor for LGALS9; the interaction retains P4HB at the cell surface of Th2 T helper cells, increasing disulfide reductase activity at the plasma membrane, altering the plasma membrane redox state and enhancing cell migration (PubMed:21670307). {ECO:0000269|PubMed:10636893, ECO:0000269|PubMed:12485997, ECO:0000269|PubMed:21670307}.; ",{"$nulls":4},"p.Trp364Leu","c.1091G>T","MODERATE","364/508",8,{"$nulls":5},"5","261","332","196","253","243","294","0","0","0","0.2517",{"$nulls":20},"4.288553","2.57","2.16;.","1","-12.3;.","1.0;.","0.001;.","0.694;0.664",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes the beta subunit of prolyl 4-hydroxylase, a highly abundant multifunctional enzyme that belongs to the protein disulfide isomerase family. When present as a tetramer consisting of two alpha and two beta subunits, this enzyme is involved in hydroxylation of prolyl residues in preprocollagen. This enzyme is also a disulfide isomerase containing two thioredoxin domains that catalyze the formation, breakage and rearrangement of disulfide bonds. Other known functions include its ability to act as a chaperone that inhibits aggregation of misfolded proteins in a concentration-dependent manner, its ability to bind thyroid hormone, its role in both the influx and efflux of S-nitrosothiol-bound nitric oxide, and its function as a subunit of the microsomal triglyceride transfer protein complex. [provided by RefSeq, Jul 2008].  ",null,"C4317154","0/0","258,0","0","258","0/1","228,94","0.2919","322",null,"chr17:81845957:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2885"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PAQR9","chr3:142962204","PAQR9(Ter378Lext*?)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Plasma membrane progesterone (P4) receptor coupled to G proteins (PubMed:23763432, PubMed:23161870). Seems to act through a G(s) mediated pathway (PubMed:23161870). May be involved in regulating rapid P4 signaling in the nervous system (PubMed:23763432). Also binds dehydroepiandrosterone (DHEA), pregnanolone, pregnenolone and allopregnanolone (PubMed:23161870). {ECO:0000269|PubMed:23161870, ECO:0000303|PubMed:23763432}.; ",{"$nulls":4},"p.Ter378Leuext*?","c.1133G>T","HIGH","378/377",1,{"$nulls":5},"5","274","317","223","263","231","266","0","0","0","0.2782",{"$nulls":20},"2.203957",null,null,"1",{"$nulls":3},"0.009",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","271,0","0","271","0/1","229,81","0.2613","310",null,"chr3:142962204:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2852"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PAQR9","chr3:142962204","PAQR9(Ter378Lext*?)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Plasma membrane progesterone (P4) receptor coupled to G proteins (PubMed:23763432, PubMed:23161870). Seems to act through a G(s) mediated pathway (PubMed:23161870). May be involved in regulating rapid P4 signaling in the nervous system (PubMed:23763432). Also binds dehydroepiandrosterone (DHEA), pregnanolone, pregnenolone and allopregnanolone (PubMed:23161870). {ECO:0000269|PubMed:23161870, ECO:0000303|PubMed:23763432}.; ",{"$nulls":4},"p.Ter378Leuext*?","c.1133G>T","HIGH","378/377",1,{"$nulls":5},"5","274","187","223","157","229","164","0","0","0","0.372",{"$nulls":20},"2.203957",null,null,"1",{"$nulls":3},"0.009",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","271,0","0","271","0/1","122,63","0.3405","185",null,"chr3:142962204:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3631"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PC","chr11:66871758","PC(Q74fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pyruvate carboxylase deficiency (PC deficiency) [MIM:266150]: Leads to lactic acidosis, mental retardation and death. It occurs in three forms: mild or type A, severe neonatal or type B, and a very mild lacticacidemia. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Pyruvate carboxylase catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second. Catalyzes in a tissue specific manner, the initial reactions of glucose (liver, kidney) and lipid (adipose tissue, liver, brain) synthesis from pyruvate.; ","mito100|mitocarta",{"$nulls":3},"p.Gln74fs","c.221_249delAGATGCACCGGCAGAAAGCAGATGAAGCC","HIGH","74/1178",3,{"$nulls":5},"3",null,null,"687","848","798","1015",null,null,"0","0.0887",{"$nulls":5},"(PC|ENSG00000173599|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Pyruvate carboxylase deficiency","Biochemical; Neurologic",{"$nulls":3},"C0034341","0/0","1059,0","0","1059","0/1","1180,100","0.0781","1280",null,"chr11:66871758:AGGCTTCATCTGCTTTCTGCCGGTGCATCT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0873"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PC","chr11:66871758","PC(Q74fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Pyruvate carboxylase deficiency (PC deficiency) [MIM:266150]: Leads to lactic acidosis, mental retardation and death. It occurs in three forms: mild or type A, severe neonatal or type B, and a very mild lacticacidemia. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Pyruvate carboxylase catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second. Catalyzes in a tissue specific manner, the initial reactions of glucose (liver, kidney) and lipid (adipose tissue, liver, brain) synthesis from pyruvate.; ","mito100|mitocarta",{"$nulls":3},"p.Gln74fs","c.221_249delAGATGCACCGGCAGAAAGCAGATGAAGCC","HIGH","74/1178",3,{"$nulls":5},"5","902","709","687","529","797","656","0.0009","0.0009","0","0.1616",{"$nulls":5},"(PC|ENSG00000173599|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Pyruvate carboxylase deficiency","Biochemical; Neurologic",{"$nulls":3},"C0034341","0/0","1059,0","0","1059","0/1","688,108","0.1357","796",null,"chr11:66871758:AGGCTTCATCTGCTTTCTGCCGGTGCATCT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1437"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PCDHB9","chr5:141188837","PCDHB9(N507Y)",null,null,"topological domain (Extracellular ), domain (Cadherin 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Asn507Tyr","c.1519A>T","MODERATE","507/797",1,{"$nulls":5},"4","584","585","454","440","511","411","0","0","0","0.1946",{"$nulls":20},"2.789692",{"$nulls":6},"0.508",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","582,0","0","582","0/1","479,88","0.1552","567",null,"chr5:141188837:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1545"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PCDHB9","chr5:141188837","PCDHB9(N507Y)",null,null,"topological domain (Extracellular ), domain (Cadherin 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.; ",{"$nulls":4},"p.Asn507Tyr","c.1519A>T","MODERATE","507/797",1,{"$nulls":5},"4","584","430","454","318","509","347","0","0","0","0.2277",{"$nulls":20},"2.789692",{"$nulls":6},"0.508",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008].",null,null,"0/0","581,0","0","581","0/1","320,93","0.2252","413",null,"chr5:141188837:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2138"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PDE3A","chr12:20646478","PDE3A(Splicing Acceptor/Donor Loss)",{"$nulls":3},"active-site:Proton_donor, metal-binding-site:Divalent_metal_cation_1","LOW, LOW",null,94.2222,"PASS","Splice-site Loss",null,-1,"DISEASE: Hypertension and brachydactyly syndrome (HTNB) [MIM:112410]: A syndrome characterized by brachydactyly type E, severe salt-independent but age-dependent hypertension, an increased fibroblast growth rate, neurovascular contact at the rostral-ventrolateral medulla, and altered baroreflex blood pressure regulation. It results in death from stroke before age 50 years when untreated. Brachydactyly type E is characterized by shortening of the fingers mainly in the metacarpals and metatarsals. {ECO:0000269|PubMed:25961942}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cyclic nucleotide phosphodiesterase with a dual- specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. {ECO:0000250|UniProtKB:Q9Z0X4}.; ",{"$nulls":4},"p.Tyr751_Thr758delinsSer","c.2252-11_2272delACTGGTTACAGATCATAACAGAATCCATGCCA","HIGH","751/1141",11,{"$nulls":5},"3",null,null,"335","638",{"$nulls":37},"Unknown",-1,{"$nulls":6},"C1862170","0/0","443,0","0","443","0/1","849,53","0.0588","902",null,"chr12:20646478:CACTGGTTACAGATCATAACAGAATCCATGCCA:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0674"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PDE4DIP","chr1:149012692","PDE4DIP(L1864F)",null,null,"coiled-coil region , splice variant (In isoform 8 and isoform 11. ), splice variant (In isoform 9, isoform 10 and isoform 12. ), splice variant (In isoform 13. ), splice variant (In isoform 2 and isoform 6. ), splice variant (In isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving PDE4DIP may be the cause of a myeloproliferative disorder (MBD) associated with eosinophilia. Translocation t(1;5)(q23;q33) that forms a PDE4DIP- PDGFRB fusion protein. {ECO:0000269|PubMed:12907457}.; ","FUNCTION: Functions as an anchor sequestering components of the cAMP-dependent pathway to Golgi and/or centrosomes (By similarity). {ECO:0000250|UniProtKB:Q9WUJ3}.; ","gedi|level2",{"$nulls":3},"p.Leu1864Phe","c.5590C>T","MODERATE","1864/2482",35,{"$nulls":5},"4",null,null,"165","215","221","164",null,null,"0","0.0732",{"$nulls":20},"1.721464",".;.;4.66;4.66",null,null,".;.;-1.31;-1.31",null,".;.;0.101;0.103","0.287;0.309;0.295;0.247",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC","The protein encoded by this gene serves to anchor phosphodiesterase 4D to the Golgi/centrosome region of the cell. Defects in this gene may be a cause of myeloproliferative disorder (MBD) associated with eosinophilia. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2010].",null,null,"0/0","237,0","0","237","0/1","289,24","0.0767","313",null,"chr1:149012692:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0791"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PDIA3","chr15:43766810","PDIA3(E310K)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,{"$nulls":7},"c.928G>A","HIGH",null,8,{"$nulls":5},"4","499","568","436","485",null,null,"0","0",{"$nulls":22},"3.767421","2.56","2.89","1","-3.12","0.348","0.029","0.648",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","499,0","0","499","0/1","423,145","0.2553","568",null,"chr15:43766810:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2536"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PDIA3","chr15:43766810","PDIA3(E310K)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,{"$nulls":7},"c.928G>A","HIGH",null,8,{"$nulls":5},"4","499","378","436","333",null,null,"0","0",{"$nulls":22},"3.767421","2.56","2.89","1","-3.12","0.348","0.029","0.648",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","499,0","0","499","0/1","194,179","0.4799","373",null,"chr15:43766810:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4565"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PHF7","chr3:52412884","PHF7(K2R)",{"$nulls":3},"antibody-mapping:heterologous_protein_expression_evidence","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in spermatogenesis.; ",{"$nulls":4},"p.Lys2Arg","c.5A>G","MODERATE","2/381",2,{"$nulls":5},"5","176","173","157","153","127","121","0","0","0","0.0661",{"$nulls":20},"2.466916","-2.05;-3.07;.","0.6","0.945383","0.03;0.08;.","0.001;.;.","0.257;0.255;.","0.191;0.141;0.229",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","176,0","0","176","0/1","162,9","0.0526","171",null,"chr3:52412884:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0523"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PIP5K1A","chr1:151242189","PIP5K1A(G477D)",{"$nulls":6},255,"PASS","Missense","rs1345729881",-1,null,"FUNCTION: Catalyzes the phosphorylation of phosphatidylinositol 4- phosphate (PtdIns4P) to form phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). PtdIns(4,5)P2 is involved in a variety of cellular processes and is the substrate to form phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3), another second messenger. The majority of PtdIns(4,5)P2 is thought to occur via type I phosphatidylinositol 4-phosphate 5-kinases given the abundance of PtdIns4P. Participates in a variety of cellular processes such as actin cytoskeleton organization, cell adhesion, migration and phagocytosis. Required for membrane ruffling formation, actin organization and focal adhesion formation during directional cell migration by controlling integrin-induced translocation of RAC1 to the plasma membrane. Together with PIP5K1C is required for phagocytosis, but they regulate different types of actin remodeling at sequential steps. Promotes particle ingestion by activating WAS that induces Arp2/3 dependent actin polymerization at the nascent phagocytic cup. Together with PIP5K1B is required after stimulation of G-protein coupled receptors for stable platelet adhesion. Plays a role during calcium-induced keratinocyte differentiation. Recruited to the plasma membrane by the E-cadherin/beta-catenin complex where it provides the substrate PtdIns(4,5)P2 for the production of PtdIns(3,4,5)P3, diacylglycerol and inositol 1,4,5-trisphosphate that mobilize internal calcium and drive keratinocyte differentiation. Together with PIP5K1C have a role during embryogenesis. Functions also in the nucleus where acts as an activator of TUT1 adenylyltransferase activity in nuclear speckles, thereby regulating mRNA polyadenylation of a select set of mRNAs (PubMed:18288197, PubMed:19158393, PubMed:20660631). Positively regulates insulin-induced translocation of SLC2A4 to the cell membrane in adipocytes (By similarity). {ECO:0000250|UniProtKB:P70182, ECO:0000269|PubMed:18288197, ECO:0000269|PubMed:19158393, ECO:0000269|PubMed:20660631}.; ",{"$nulls":4},"p.Gly477Asp","c.1430G>A","MODERATE","477/562",13,{"$nulls":5},"5","372","265","313","216","297","221","0","0","0","0.0588",{"$nulls":20},"2.04005","1.73;1.7;1.42;1.71",".;.;.;1.79","0.907399;0.907399;0.942104;0.907399;1;1","-1.22;-1.22;-1.18;-1.22","0.328;.;0.677;0.001","0.15;0.144;0.153;0.113","0.365;0.373;0.394;0.378",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","370,0","0","370","0/1","247,14","0.0536","261",null,"chr1:151242189:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0602"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PKHD1","chr6:51746758","PKHD1(D3321N)",null,null,"topological domain (Extracellular ), sequence variant (Found in a patient affected by polycystic liver disease; unknown pathological significance. ), sequence variant (Probable disease-associated variant found in a patient affected by polycystic liver disease. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Loss-of-function PKHD1 variations may cause autosomal dominant polycystic liver disease (PCLD) in patients that lack variations in known causative genes, such as PRKCSH and SEC63. {ECO:0000269|PubMed:28375157}.; ","FUNCTION: May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation. {ECO:0000269|PubMed:20554582}.; ",{"$nulls":4},"p.Asp3321Asn","c.9961G>A","MODERATE","3321/4074",59,{"$nulls":5},"5","467","499","341","365","389","398","0","0","0","0.2663",{"$nulls":20},"3.747839","-2.09;-2.31","2.595","0.948024","-2.48;-2.65","0.999;0.996","0.016;0.018","0.164;0.178",{"$nulls":3},"Unknown",-1,"AR","Polycystic kidney disease, autosomal recessive","Allergy/Immunology/Infectious; Endocrine; Gastrointestinal; Renal",{"$nulls":3},"C0085548","0/0","454,0","0","454","0/1","365,114","0.238","479",null,"chr6:51746758:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2329"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PKHD1","chr6:51746758","PKHD1(D3321N)",null,null,"topological domain (Extracellular ), sequence variant (Found in a patient affected by polycystic liver disease; unknown pathological significance. ), sequence variant (Probable disease-associated variant found in a patient affected by polycystic liver disease. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Loss-of-function PKHD1 variations may cause autosomal dominant polycystic liver disease (PCLD) in patients that lack variations in known causative genes, such as PRKCSH and SEC63. {ECO:0000269|PubMed:28375157}.; ","FUNCTION: May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation. {ECO:0000269|PubMed:20554582}.; ",{"$nulls":4},"p.Asp3321Asn","c.9961G>A","MODERATE","3321/4074",59,{"$nulls":5},"5","467","231","341","175","388","181","0","0","0","0.5691",{"$nulls":20},"3.747839","-2.09;-2.31","2.595","0.948024","-2.48;-2.65","0.999;0.996","0.016;0.018","0.164;0.178",{"$nulls":3},"Unknown",-1,"AR","Polycystic kidney disease, autosomal recessive","Allergy/Immunology/Infectious; Endocrine; Gastrointestinal; Renal",{"$nulls":3},"C0085548","0/0","459,0","0","459","0/1","90,136","0.6018","226",null,"chr6:51746758:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5829"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PKP1","chr1:201316686","PKP1(A279P)",{"$nulls":3},"helix:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Seems to play a role in junctional plaques. Contributes to epidermal morphogenesis. {ECO:0000269|PubMed:9326952}.; ",{"$nulls":4},"p.Ala279Pro","c.835G>C","MODERATE","279/747",4,{"$nulls":5},"5","395","493","263","327","362","445","0","0","0","0.218",{"$nulls":20},"4.317726","-0.28","2.93","1","-4.44","0.966;0.999;0.999","0.002","0.919;0.856;0.856",{"$nulls":3},"Unknown",-1,"AR","Ectodermal dysplasia/skin fragility syndrome","Dermatologic",null,"This gene encodes a member of the arm-repeat (armadillo) and plakophilin gene families. Plakophilin proteins contain numerous armadillo repeats, localize to cell desmosomes and nuclei, and participate in linking cadherins to intermediate filaments in the cytoskeleton. This protein may be involved in molecular recruitment and stabilization during desmosome formation. Mutations in this gene have been associated with the ectodermal dysplasia/skin fragility syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010].",null,"C1858302","0/0","383,0","0","383","0/1","365,112","0.2348","477",null,"chr1:201316686:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2263"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PKP1","chr1:201316686","PKP1(A279P)",{"$nulls":3},"helix:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Seems to play a role in junctional plaques. Contributes to epidermal morphogenesis. {ECO:0000269|PubMed:9326952}.; ",{"$nulls":4},"p.Ala279Pro","c.835G>C","MODERATE","279/747",4,{"$nulls":5},"5","395","184","263","121","360","161","0","0","0","0.7019",{"$nulls":20},"4.317726","-0.28","2.93","1","-4.44","0.966;0.999;0.999","0.002","0.919;0.856;0.856",{"$nulls":3},"Unknown",-1,"AR","Ectodermal dysplasia/skin fragility syndrome","Dermatologic",null,"This gene encodes a member of the arm-repeat (armadillo) and plakophilin gene families. Plakophilin proteins contain numerous armadillo repeats, localize to cell desmosomes and nuclei, and participate in linking cadherins to intermediate filaments in the cytoskeleton. This protein may be involved in molecular recruitment and stabilization during desmosome formation. Mutations in this gene have been associated with the ectodermal dysplasia/skin fragility syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010].",null,"C1858302","0/0","387,0","0","387","0/1","56,126","0.6923","182",null,"chr1:201316686:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7107"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PLAGL2","chr20:32197199","PLAGL2(K248N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Shows weak transcriptional activatory activity.; ",{"$nulls":4},"p.Lys248Asn","c.744G>C","MODERATE","248/496",3,1,{"$nulls":4},"5","648","564","526","463","528","466","0","0","0","0.1824",{"$nulls":20},"2.811397","2.9","1.935","0.99921","-2.58","0.991",null,"0.397",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","641,0","0","641","0/1","450,104","0.1877","554",null,"chr20:32197199:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1901"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PLCZ1","chr12:18683244","PLCZ1(R608G)",{"$nulls":6},255,"PASS","Missense","rs1257019153",-1,"DISEASE: Spermatogenic failure 17 (SPGF17) [MIM:617214]: An autosomal recessive infertility disorder due to failure of oocyte activation and fertilization by sperm that otherwise exhibits normal morphology. {ECO:0000269|PubMed:26721930}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. In vitro, hydrolyzes PtdIns(4,5)P2 in a Ca(2+)- dependent manner. Triggers intracellular Ca(2+) oscillations in oocytes solely during M phase and is involved in inducing oocyte activation and initiating embryonic development up to the blastocyst stage. Is therefore a strong candidate for the egg- activating soluble sperm factor that is transferred from the sperm into the egg cytoplasm following gamete membrane fusion. May exert an inhibitory effect on phospholipase-C-coupled processes that depend on calcium ions and protein kinase C, including CFTR trafficking and function. {ECO:0000250|UniProtKB:Q8K4D7, ECO:0000269|PubMed:12416999, ECO:0000269|PubMed:14697805, ECO:0000269|PubMed:15579586, ECO:0000269|PubMed:26721930, ECO:0000305}.; ",{"$nulls":4},"p.Arg608Gly","c.1822A>G","MODERATE","608/608",15,{"$nulls":5},"5","366","738","274","522","309","602","0","0","0","0.1163",{"$nulls":20},"2.206876",".;1.4;2.81;2.12;1.81",".;.;.;1.61;.","1;1;1;1;1;1;0.999998",".;-1.59;-2.16;-1.87;-1.91",".;.;0.421;0.281;.",".;0.002;0.004;0.003;0.002",".;0.316;0.25;0.305;0.263",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310666","0/0","361,0","0","361","0/1","648,75","0.1037","723",null,"chr12:18683244:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0996"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PLCZ1","chr12:18683244","PLCZ1(R608G)",{"$nulls":6},255,"PASS","Missense","rs1257019153",-1,"DISEASE: Spermatogenic failure 17 (SPGF17) [MIM:617214]: An autosomal recessive infertility disorder due to failure of oocyte activation and fertilization by sperm that otherwise exhibits normal morphology. {ECO:0000269|PubMed:26721930}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. In vitro, hydrolyzes PtdIns(4,5)P2 in a Ca(2+)- dependent manner. Triggers intracellular Ca(2+) oscillations in oocytes solely during M phase and is involved in inducing oocyte activation and initiating embryonic development up to the blastocyst stage. Is therefore a strong candidate for the egg- activating soluble sperm factor that is transferred from the sperm into the egg cytoplasm following gamete membrane fusion. May exert an inhibitory effect on phospholipase-C-coupled processes that depend on calcium ions and protein kinase C, including CFTR trafficking and function. {ECO:0000250|UniProtKB:Q8K4D7, ECO:0000269|PubMed:12416999, ECO:0000269|PubMed:14697805, ECO:0000269|PubMed:15579586, ECO:0000269|PubMed:26721930, ECO:0000305}.; ",{"$nulls":4},"p.Arg608Gly","c.1822A>G","MODERATE","608/608",15,{"$nulls":5},"5","366","828","274","590","311","691","0","0","0","0.1259",{"$nulls":20},"2.206876",".;1.4;2.81;2.12;1.81",".;.;.;1.61;.","1;1;1;1;1;1;0.999998",".;-1.59;-2.16;-1.87;-1.91",".;.;0.421;0.281;.",".;0.002;0.004;0.003;0.002",".;0.316;0.25;0.305;0.263",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310666","0/0","363,0","0","363","0/1","705,96","0.1199","801",null,"chr12:18683244:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1102"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","POMGNT1","chr1:46192343","POMGNT1(E460*)",null,null,"topological domain (Lumenal ), region of interest (Catalytic ), disulfide bond , helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A3 (MDDGA3) [MIM:253280]: An autosomal recessive disorder characterized by congenital muscular dystrophy, ocular abnormalities, cobblestone lissencephaly, and cerebellar and pontine hypoplasia. Patients present severe congenital myopia, congenital glaucoma, pallor of the optic disks, retinal hypoplasia, mental retardation, hydrocephalus, abnormal electroencephalograms, generalized muscle weakness and myoclonic jerks. Included diseases are the more severe Walker-Warburg syndrome and the slightly less severe muscle-eye-brain disease. {ECO:0000269|PubMed:11709191, ECO:0000269|PubMed:12588800, ECO:0000269|PubMed:12788071, ECO:0000269|PubMed:15207699, ECO:0000269|PubMed:15236414, ECO:0000269|PubMed:15466003, ECO:0000269|PubMed:17030669, ECO:0000269|PubMed:19067344}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Muscular dystrophy-dystroglycanopathy congenital with mental retardation B3 (MDDGB3) [MIM:613151]: An autosomal recessive disorder characterized by congenital muscular dystrophy associated with mental retardation and mild structural brain abnormalities. Clinical features include mental retardation, white matter changes, cerebellar cysts, pontine hypoplasia, myopia, optic atrophy, decreased alpha-dystroglycan on muscle biopsy and increased serum creatine kinase. {ECO:0000269|PubMed:17030669, ECO:0000269|PubMed:19067344, ECO:0000269|PubMed:19299310}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Muscular dystrophy-dystroglycanopathy limb-girdle C3 (MDDGC3) [MIM:613157]: A rare form of limb-girdle muscular dystrophy with normal cognition. Muscle biopsy shows dystrophic changes with variable staining for glycosylated alpha- dystroglycan. {ECO:0000269|PubMed:18195152}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinitis pigmentosa 76 (RP76) [MIM:617123]: A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP76 inheritance is autosomal recessive. {ECO:0000269|PubMed:26908613, ECO:0000269|PubMed:27391550}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Participates in O-mannosyl glycosylation by catalyzing the addition of N-acetylglucosamine to O-linked mannose on glycoproteins (PubMed:11709191, PubMed:27493216). Catalyzes the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moiety on alpha-dystroglycan and other O-mannosylated proteins, providing the necessary basis for the addition of further carbohydrate moieties (PubMed:11709191, PubMed:27493216). Is specific for alpha linked terminal mannose and does not have MGAT3, MGAT4, MGAT5, MGAT7 or MGAT8 activity. {ECO:0000269|PubMed:11709191, ECO:0000269|PubMed:11742540, ECO:0000269|PubMed:26908613, ECO:0000269|PubMed:27391550, ECO:0000269|PubMed:27493216}.; ",{"$nulls":4},"p.Glu460*","c.1378G>T","HIGH","460/748",16,{"$nulls":5},"4","921","998","721","718","828","859","0","0","0","0.135",{"$nulls":5},"(POMGNT1|ENSG00000085998|1|1.00)","(POMGNT1|ENSG00000085998|1|1.00)",{"$nulls":13},"7.903507",null,null,"1",{"$nulls":3},"0.831;0.781",{"$nulls":3},"Unknown",-1,"AR","Congenital muscular dystrophy with brain and eye anomalies, type A, 3; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 3; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 3","Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic",{"$nulls":3},"C4310704| C0457133| C3150412| C3150417","0/0","904,1","0.0011","905","0/1","814,134","0.1414","948",null,"chr1:46192343:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1407"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PPP1R15A","chr19:48875872","PPP1R15A(S642T)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Recruits the serine/threonine-protein phosphatase PP1 to dephosphorylate the translation initiation factor eIF-2A/EIF2S1, thereby reversing the shut-off of protein synthesis initiated by stress-inducible kinases and facilitating recovery of cells from stress. Down-regulates the TGF-beta signaling pathway by promoting dephosphorylation of TGFB1 by PP1. May promote apoptosis by inducing TP53 phosphorylation on 'Ser-15'. {ECO:0000269|PubMed:11564868, ECO:0000269|PubMed:12556489, ECO:0000269|PubMed:14635196, ECO:0000269|PubMed:14718519, ECO:0000269|PubMed:8139541}.; ",{"$nulls":4},"p.Ser642Thr","c.1924T>A","MODERATE","642/674",3,{"$nulls":5},"5","222","216","147","145","194","195","0","0","0","0.3487",{"$nulls":20},"-0.308871","3.13","1.79","1","-0.16","0.004","0.329","0.126",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","209,0","0","209","0/1","133,70","0.3448","203",null,"chr19:48875872:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3448"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PPP1R15A","chr19:48875872","PPP1R15A(S642T)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Recruits the serine/threonine-protein phosphatase PP1 to dephosphorylate the translation initiation factor eIF-2A/EIF2S1, thereby reversing the shut-off of protein synthesis initiated by stress-inducible kinases and facilitating recovery of cells from stress. Down-regulates the TGF-beta signaling pathway by promoting dephosphorylation of TGFB1 by PP1. May promote apoptosis by inducing TP53 phosphorylation on 'Ser-15'. {ECO:0000269|PubMed:11564868, ECO:0000269|PubMed:12556489, ECO:0000269|PubMed:14635196, ECO:0000269|PubMed:14718519, ECO:0000269|PubMed:8139541}.; ",{"$nulls":4},"p.Ser642Thr","c.1924T>A","MODERATE","642/674",3,{"$nulls":5},"5","222","117","147","80","199","99","0","0","0","0.7576",{"$nulls":20},"-0.308871","3.13","1.79","1","-0.16","0.004","0.329","0.126",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","208,0","0","208","0/1","23,85","0.787","108",null,"chr19:48875872:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.775"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PPP1R15A","chr19:48875920","PPP1R15A(R658S)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Recruits the serine/threonine-protein phosphatase PP1 to dephosphorylate the translation initiation factor eIF-2A/EIF2S1, thereby reversing the shut-off of protein synthesis initiated by stress-inducible kinases and facilitating recovery of cells from stress. Down-regulates the TGF-beta signaling pathway by promoting dephosphorylation of TGFB1 by PP1. May promote apoptosis by inducing TP53 phosphorylation on 'Ser-15'. {ECO:0000269|PubMed:11564868, ECO:0000269|PubMed:12556489, ECO:0000269|PubMed:14635196, ECO:0000269|PubMed:14718519, ECO:0000269|PubMed:8139541}.; ",{"$nulls":4},"p.Arg658Ser","c.1972C>A","MODERATE","658/674",3,1,{"$nulls":4},"5","153","140","103","93","132","121","0","0","0","0.2727",{"$nulls":20},"-0.070235","3.51","-0.55","1","0.21",null,"0.973","0.118",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","146,0","0","146","0/1","94,40","0.2985","134",null,"chr19:48875920:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2796"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PPP1R15A","chr19:48875920","PPP1R15A(R658S)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Recruits the serine/threonine-protein phosphatase PP1 to dephosphorylate the translation initiation factor eIF-2A/EIF2S1, thereby reversing the shut-off of protein synthesis initiated by stress-inducible kinases and facilitating recovery of cells from stress. Down-regulates the TGF-beta signaling pathway by promoting dephosphorylation of TGFB1 by PP1. May promote apoptosis by inducing TP53 phosphorylation on 'Ser-15'. {ECO:0000269|PubMed:11564868, ECO:0000269|PubMed:12556489, ECO:0000269|PubMed:14635196, ECO:0000269|PubMed:14718519, ECO:0000269|PubMed:8139541}.; ",{"$nulls":4},"p.Arg658Ser","c.1972C>A","MODERATE","658/674",3,1,{"$nulls":4},"5","153","83","103","57","131","70","0","0","0","0.7714",{"$nulls":20},"-0.070235","3.51","-0.55","1","0.21",null,"0.973","0.118",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","146,0","0","146","0/1","18,65","0.7831","83",null,"chr19:48875920:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7544"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PPWD1","chr5:65563324","PPWD1(S5I)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). May be involved in pre- mRNA splicing (PubMed:11991638). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:20676357}.; ",{"$nulls":4},"p.Ser5Ile","c.14G>T","MODERATE","5/646",1,{"$nulls":5},"4","72","73","69","64",null,null,"0","0",{"$nulls":22},"1.441163","0.05","0.345","0.998335;0.998335;1","-0.18","0.01","0.262","0.152",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","74,0","0","74","0/1","57,18","0.24","75",null,"chr5:65563324:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.25"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PREX1","chr20:48627607","PREX1(R1626S)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.; ",{"$nulls":4},"p.Arg1626Ser","c.4878G>C","MODERATE","1626/1659",39,{"$nulls":5},"4","405","456","281","314","385","434","0","0","0","0.053",{"$nulls":20},"2.857848","-1.22","2.215","0.999931;1","-3.39","0.867","0.065","0.946",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","383,0","0","383","0/1","411,24","0.0552","435",null,"chr20:48627607:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0541"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PREX1","chr20:48676242","PREX1(Y539C)",null,null,"domain (DEP 2 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a RAC guanine nucleotide exchange factor (GEF), which activates the Rac proteins by exchanging bound GDP for free GTP. Its activity is synergistically activated by phosphatidylinositol 3,4,5-trisphosphate and the beta gamma subunits of heterotrimeric G protein. May function downstream of heterotrimeric G proteins in neutrophils.; ",{"$nulls":4},"p.Tyr539Cys","c.1616A>G","MODERATE","539/1659",14,{"$nulls":5},"5","533","705","380","479","464","606","0","0","0","0.1172",{"$nulls":20},"4.282987","2.08","2.5","0.999987","-5.56","1.0",null,"0.933",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","504,0","0","504","0/1","584,82","0.1231","666",null,"chr20:48676242:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1253"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PRUNE2","chr9:76707901","PRUNE2(V1458G)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play an important role in regulating differentiation, survival and aggressiveness of the tumor cells. {ECO:0000269|PubMed:16288218}.; ",{"$nulls":4},"p.Val1458Gly","c.4373T>G","MODERATE","1458/3088",8,{"$nulls":5},"4","354","427","287","332","316","375","0","0","0","0.0933",{"$nulls":20},"1.240165","0.85;.;0.85","1.1;.;.","1","-1.54;.;-1.45","0.091;.;.","0.003;.;0.003","0.226;0.164;0.216",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","356,0","0","356","0/1","370,51","0.1211","421",null,"chr9:76707901:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1054"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PRUNE2","chr9:76707901","PRUNE2(V1458G)",null,null,"splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play an important role in regulating differentiation, survival and aggressiveness of the tumor cells. {ECO:0000269|PubMed:16288218}.; ",{"$nulls":4},"p.Val1458Gly","c.4373T>G","MODERATE","1458/3088",8,{"$nulls":5},"4","354","314","287","260","314","269","0","0","0","0.342",{"$nulls":20},"1.240165","0.85;.;0.85","1.1;.;.","1","-1.54;.;-1.45","0.091;.;.","0.003;.;0.003","0.226;0.164;0.216",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","356,0","0","356","0/1","205,106","0.3408","311",null,"chr9:76707901:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3462"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PSTPIP2","chr18:46039966","PSTPIP2(E39K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to F-actin. May be involved in regulation of the actin cytoskeleton (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu39Lys","c.115G>A","MODERATE","39/334",2,{"$nulls":5},"5","511","501","368","350","455","436","0","0","0","0.0642",{"$nulls":20},"4.370801","2.32","2.355","0.999465",".;-3.77","1.0",".;0.0","0.533;0.592",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","507,0","0","507","0/1","453,34","0.0698","487",null,"chr18:46039966:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.06"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PTDSS1","chr8:96320289","PTDSS1(Q373*)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lenz-Majewski hyperostotic dwarfism (LMHD) [MIM:151050]: A syndrome of intellectual disability and multiple congenital anomalies that features generalized craniotubular hyperostosis. LMHD is characterized by the combination of sclerosing bone dysplasia, intellectual disability and distinct craniofacial, dental, cutaneous and distal limb anomalies. The progressive generalized hyperostosis associated with this syndrome affects the cranium, the vertebrae and the diaphyses of tubular bones, leading to severe growth restriction. {ECO:0000269|PubMed:24241535}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes a base-exchange reaction in which the polar head group of phosphatidylethanolamine (PE) or phosphatidylcholine (PC) is replaced by L-serine. In membranes, PTDSS1 catalyzes mainly the conversion of phosphatidylcholine. Also converts, in vitro and to a lesser extent, phosphatidylethanolamine.; ",{"$nulls":4},"p.Gln373*","c.1117C>T","HIGH","373/473",10,{"$nulls":5},"5","446","509","348","354","382","449","0","0","0","0.098",{"$nulls":5},"(PTDSS1|ENSG00000156471|1|1.00)","(PTDSS1|ENSG00000156471|1|1.00)",{"$nulls":13},"8.865476",null,null,"1",{"$nulls":3},"0.551;0.621",{"$nulls":3},"Unknown",-1,"AD","Lenz-Majewski hyperostotic dwarfism","Craniofacial; Dental; Genitourinary; Musculoskeletal; Neurologic",{"$nulls":3},"C0432269","0/0","443,0","0","443","0/1","438,46","0.095","484",null,"chr8:96320289:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0876"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PTDSS1","chr8:96320289","PTDSS1(Q373*)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lenz-Majewski hyperostotic dwarfism (LMHD) [MIM:151050]: A syndrome of intellectual disability and multiple congenital anomalies that features generalized craniotubular hyperostosis. LMHD is characterized by the combination of sclerosing bone dysplasia, intellectual disability and distinct craniofacial, dental, cutaneous and distal limb anomalies. The progressive generalized hyperostosis associated with this syndrome affects the cranium, the vertebrae and the diaphyses of tubular bones, leading to severe growth restriction. {ECO:0000269|PubMed:24241535}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes a base-exchange reaction in which the polar head group of phosphatidylethanolamine (PE) or phosphatidylcholine (PC) is replaced by L-serine. In membranes, PTDSS1 catalyzes mainly the conversion of phosphatidylcholine. Also converts, in vitro and to a lesser extent, phosphatidylethanolamine.; ",{"$nulls":4},"p.Gln373*","c.1117C>T","HIGH","373/473",10,{"$nulls":5},"5","446","408","348","294","380","339","0","0","0","0.1888",{"$nulls":5},"(PTDSS1|ENSG00000156471|1|1.00)","(PTDSS1|ENSG00000156471|1|1.00)",{"$nulls":13},"8.865476",null,null,"1",{"$nulls":3},"0.551;0.621",{"$nulls":3},"Unknown",-1,"AD","Lenz-Majewski hyperostotic dwarfism","Craniofacial; Dental; Genitourinary; Musculoskeletal; Neurologic",{"$nulls":3},"C0432269","0/0","444,0","0","444","0/1","325,77","0.1915","402",null,"chr8:96320289:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1973"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","PYGL","chr14:50944328","PYGL(A26T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glycogen storage disease 6 (GSD6) [MIM:232700]: A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected. {ECO:0000269|PubMed:9529348}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.; ",{"$nulls":4},"p.Ala26Thr","c.76G>A","MODERATE","26/847",1,{"$nulls":5},"5","751","611","513","403","688","555","0","0","0","0.1784",{"$nulls":20},"2.541223","-2.48",".;0.975;0.975","1","-0.2;-0.3;-0.25",".;.;0.001","0.602;0.589;0.619","0.491;0.51;0.434",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease VI","Biochemical",{"$nulls":3},"C0017925","0/0","728,0","0","728","0/1","475,105","0.181","580",null,"chr14:50944328:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1712"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","PYGL","chr14:50944328","PYGL(A26T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glycogen storage disease 6 (GSD6) [MIM:232700]: A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected. {ECO:0000269|PubMed:9529348}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.; ",{"$nulls":4},"p.Ala26Thr","c.76G>A","MODERATE","26/847",1,{"$nulls":5},"5","751","247","513","180","683","190","0","0","0","0.5632",{"$nulls":20},"2.541223","-2.48",".;0.975;0.975","1","-0.2;-0.3;-0.25",".;.;0.001","0.602;0.589;0.619","0.491;0.51;0.434",{"$nulls":3},"Unknown",-1,"AR","Glycogen storage disease VI","Biochemical",{"$nulls":3},"C0017925","0/0","728,0","0","728","0/1","96,141","0.5949","237",null,"chr14:50944328:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5611"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RAPGEF2","chr4:159322470","RAPGEF2(N165T)",null,null,"nucleotide phosphate-binding region (cNMP )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions as a guanine nucleotide exchange factor (GEF), which activates Rap and Ras family of small GTPases by exchanging bound GDP for free GTP in a cAMP-dependent manner. Serves as a link between cell surface receptors and Rap/Ras GTPases in intracellular signaling cascades. Acts also as an effector for Rap1 by direct association with Rap1-GTP thereby leading to the amplification of Rap1-mediated signaling. Shows weak activity on HRAS. It is controversial whether RAPGEF2 binds cAMP and cGMP (PubMed:23800469, PubMed:10801446) or not (PubMed:10608844, PubMed:10548487, PubMed:11359771). Its binding to ligand-activated beta-1 adrenergic receptor ADRB1 leads to the Ras activation through the G(s)-alpha signaling pathway. Involved in the cAMP- induced Ras and Erk1/2 signaling pathway that leads to sustained inhibition of long term melanogenesis by reducing dendrite extension and melanin synthesis. Provides also inhibitory signals for cell proliferation of melanoma cells and promotes their apoptosis in a cAMP-independent nanner. Regulates cAMP-induced neuritogenesis by mediating the Rap1/B-Raf/ERK signaling through a pathway that is independent on both PKA and RAPGEF3/RAPGEF4. Involved in neuron migration and in the formation of the major forebrain fiber connections forming the corpus callosum, the anterior commissure and the hippocampal commissure during brain development. Involved in neuronal growth factor (NGF)-induced sustained activation of Rap1 at late endosomes and in brain- derived neurotrophic factor (BDNF)-induced axon outgrowth of hippocampal neurons. Plays a role in the regulation of embryonic blood vessel formation and in the establishment of basal junction integrity and endothelial barrier function. May be involved in the regulation of the vascular endothelial growth factor receptor KDR and cadherin CDH5 expression at allantois endothelial cell-cell junctions. {ECO:0000269|PubMed:10548487, ECO:0000269|PubMed:10608844, ECO:0000269|PubMed:10608883, ECO:0000269|PubMed:10801446, ECO:0000269|PubMed:10934204, ECO:0000269|PubMed:11359771, ECO:0000269|PubMed:12391161, ECO:0000269|PubMed:16272156, ECO:0000269|PubMed:17724123, ECO:0000269|PubMed:21840392, ECO:0000269|PubMed:23800469}.; ","level2",{"$nulls":3},"p.Asn165Thr","c.494A>C","MODERATE","165/1499",4,{"$nulls":5},"5","311","270","211","191","278","243","0","0","0","0.0658",{"$nulls":20},"2.697083",".;.;-1.8;-3.05;-1.8",".;.;.;1.665;.","1",".;.;-3.53;-3.2;-3.53",".;.;.;0.051;.",".;.;0.096;0.167;0.073",".;.;.;0.354;.",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",null,null,"C4748080","0/0","305,0","0","305","0/1","239,20","0.0772","259",null,"chr4:159322470:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0733"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RAPGEFL1","chr17:40191331","RAPGEFL1(V452fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Probable guanine nucleotide exchange factor (GEF).; ",{"$nulls":4},"p.Val452fs","c.1355_1386delTGTTCCACGGGGAGCGCGGCCGCCGGGAGACG","HIGH","452/662",9,{"$nulls":5},"5","406","424","290","284","284","280","0","0","0","0.1536",{"$nulls":5},"(RAPGEFL1|ENSG00000108352|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","437,0","0","437","0/1","393,57","0.1267","450",null,"chr17:40191331:TACGTGTTCCACGGGGAGCGCGGCCGCCGGGAG:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1373"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RBCK1","chr20:420991","RBCK1(E293K)",null,null,"zinc finger region (RING-type 1 ), region of interest (TRIAD supradomain ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1335750474",-1,"DISEASE: Polyglucosan body myopathy 1 with or without immunodeficiency (PGBM1) [MIM:615895]: A disease characterized by polyglucosan storage myopathy associated with early-onset progressive muscle weakness and progressive dilated cardiomyopathy, which may necessitate cardiac transplant in severe cases. Some patients present with severe immunodeficiency, invasive bacterial infections and chronic autoinflammation. {ECO:0000269|PubMed:23104095, ECO:0000269|PubMed:23798481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2L3/UBCM4, and then transfers it to substrates. Functions as an E3 ligase for oxidized IREB2 and both heme and oxygen are necessary for IREB2 ubiquitination. Promotes ubiquitination of TAB2 and IRF3 and their degradation by the proteasome. Component of the LUBAC complex which conjugates linear ('Met-1'-linked) polyubiquitin chains to substrates and plays a key role in NF- kappa-B activation and regulation of inflammation. LUBAC conjugates linear polyubiquitin to IKBKG and RIPK1 and is involved in activation of the canonical NF-kappa-B and the JNK signaling pathways. Linear ubiquitination mediated by the LUBAC complex interferes with TNF-induced cell death and thereby prevents inflammation. LUBAC is recruited to the TNF-R1 signaling complex (TNF-RSC) following polyubiquitination of TNF-RSC components by BIRC2 and/or BIRC3 and to conjugate linear polyubiquitin to IKBKG and possibly other components contributing to the stability of the complex. Together with OTULIN, the LUBAC complex regulates the canonical Wnt signaling during angiogenesis. Binds polyubiquitin of different linkage types. {ECO:0000269|PubMed:12629548, ECO:0000269|PubMed:17006537, ECO:0000269|PubMed:17449468, ECO:0000269|PubMed:18711448, ECO:0000269|PubMed:19136968, ECO:0000269|PubMed:20005846, ECO:0000269|PubMed:21455173, ECO:0000269|PubMed:21455180, ECO:0000269|PubMed:21455181}.; ",{"$nulls":4},"p.Glu293Lys","c.877G>A","MODERATE","293/510",7,1,{"$nulls":4},"5","378","249","283","186","309","194","0","0","0","0.1649",{"$nulls":20},"3.595586","0.78;-0.26","1.665;.","0.997921;0.997391;1","-3.16","0.116;0.275","0.021;0.02","0.329;0.355",{"$nulls":3},"Unknown",-1,"AR","Polyglucosan body myopathy 1","Allergy/Immunology/Infectious; Cardiovascular; Musculoskeletal; Neurologic",{"$nulls":3},"C4014605","0/0","375,0","0","375","0/1","201,42","0.1728","243",null,"chr20:420991:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1559"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RBCK1","chr20:420991","RBCK1(E293K)",null,null,"zinc finger region (RING-type 1 ), region of interest (TRIAD supradomain ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1335750474",-1,"DISEASE: Polyglucosan body myopathy 1 with or without immunodeficiency (PGBM1) [MIM:615895]: A disease characterized by polyglucosan storage myopathy associated with early-onset progressive muscle weakness and progressive dilated cardiomyopathy, which may necessitate cardiac transplant in severe cases. Some patients present with severe immunodeficiency, invasive bacterial infections and chronic autoinflammation. {ECO:0000269|PubMed:23104095, ECO:0000269|PubMed:23798481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2L3/UBCM4, and then transfers it to substrates. Functions as an E3 ligase for oxidized IREB2 and both heme and oxygen are necessary for IREB2 ubiquitination. Promotes ubiquitination of TAB2 and IRF3 and their degradation by the proteasome. Component of the LUBAC complex which conjugates linear ('Met-1'-linked) polyubiquitin chains to substrates and plays a key role in NF- kappa-B activation and regulation of inflammation. LUBAC conjugates linear polyubiquitin to IKBKG and RIPK1 and is involved in activation of the canonical NF-kappa-B and the JNK signaling pathways. Linear ubiquitination mediated by the LUBAC complex interferes with TNF-induced cell death and thereby prevents inflammation. LUBAC is recruited to the TNF-R1 signaling complex (TNF-RSC) following polyubiquitination of TNF-RSC components by BIRC2 and/or BIRC3 and to conjugate linear polyubiquitin to IKBKG and possibly other components contributing to the stability of the complex. Together with OTULIN, the LUBAC complex regulates the canonical Wnt signaling during angiogenesis. Binds polyubiquitin of different linkage types. {ECO:0000269|PubMed:12629548, ECO:0000269|PubMed:17006537, ECO:0000269|PubMed:17449468, ECO:0000269|PubMed:18711448, ECO:0000269|PubMed:19136968, ECO:0000269|PubMed:20005846, ECO:0000269|PubMed:21455173, ECO:0000269|PubMed:21455180, ECO:0000269|PubMed:21455181}.; ",{"$nulls":4},"p.Glu293Lys","c.877G>A","MODERATE","293/510",7,1,{"$nulls":4},"5","378","179","283","134","310","139","0","0","0","0.6115",{"$nulls":20},"3.595586","0.78;-0.26","1.665;.","0.997921;0.997391;1","-3.16","0.116;0.275","0.021;0.02","0.329;0.355",{"$nulls":3},"Unknown",-1,"AR","Polyglucosan body myopathy 1","Allergy/Immunology/Infectious; Cardiovascular; Musculoskeletal; Neurologic",{"$nulls":3},"C4014605","0/0","375,0","0","375","0/1","72,103","0.5886","175",null,"chr20:420991:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5896"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RDH8","chr19:10021565","RDH8(P271Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Retinol dehydrogenase with a clear preference for NADP. Converts all-trans-retinal to all-trans-retinol. May play a role in the regeneration of visual pigment at high light intensity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro271Gln","c.812C>A","MODERATE","271/331",6,{"$nulls":5},"4","1019","1375","775","1015","859","1152","0","0","0","0.1519",{"$nulls":20},"3.301146","-3.23",null,"1",{"$nulls":3},"0.681",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the short-chain dehydrogenase/reductase family. The encoded protein catalyzes the reduction of all-trans-retinal to all-trans-retinol, the first reaction step of the rhodopsin regeneration pathway. This enzymatic reaction is the rate-limiting step in the visual cycle. [provided by RefSeq, Feb 2014].  ",null,null,"0/0","993,0","0","993","0/1","1108,202","0.1542","1310",null,"chr19:10021565:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1596"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RER1","chr1:2400910","RER1(R114G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the retrieval of endoplasmic reticulum membrane proteins from the early Golgi compartment. {ECO:0000250}.; ",{"$nulls":4},"p.Arg114Gly","c.340C>G","MODERATE","114/196",4,1,{"$nulls":4},"5","423","533","305","346","385","465","0","0","0","0.2172",{"$nulls":20},"3.573468",null,null,"0.999998;0.999998;0.999998;0.999736;0.999736","1.19",null,"0.0","0.207",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","414,0","0","414","0/1","381,112","0.2272","493",null,"chr1:2400910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.211"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RER1","chr1:2400910","RER1(R114G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the retrieval of endoplasmic reticulum membrane proteins from the early Golgi compartment. {ECO:0000250}.; ",{"$nulls":4},"p.Arg114Gly","c.340C>G","MODERATE","114/196",4,1,{"$nulls":4},"5","423","349","305","240","383","316","0","0","0","0.3165",{"$nulls":20},"3.573468",null,null,"0.999998;0.999998;0.999998;0.999736;0.999736","1.19",null,"0.0","0.207",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","414,0","0","414","0/1","231,102","0.3063","333",null,"chr1:2400910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3167"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RFX4","chr12:106711491","RFX4(S334A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. {ECO:0000250|UniProtKB:Q7TNK1}.; ",{"$nulls":4},"p.Ser334Ala","c.1000T>G","MODERATE","334/744",10,{"$nulls":5},"5","422","402","290","264","386","358","0.0024","0.0024","0","0.2905",{"$nulls":20},"3.874696","0.42;.;0.42;0.42","2.04;.;.;.","0.999999","-2.63;.;-2.63;-2.63","0.841;.;0.902;.","0.018;.;0.019;0.028","0.723;.;0.75;0.743",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","414,1","0.0024","415","0/1","276,112","0.2887","388",null,"chr12:106711491:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3106"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RFX4","chr12:106711491","RFX4(S334A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. {ECO:0000250|UniProtKB:Q7TNK1}.; ",{"$nulls":4},"p.Ser334Ala","c.1000T>G","MODERATE","334/744",10,{"$nulls":5},"5","422","209","290","142","388","185","0.0024","0.0024","0","0.6865",{"$nulls":20},"3.874696","0.42;.;0.42;0.42","2.04;.;.;.","0.999999","-2.63;.;-2.63;-2.63","0.841;.;0.902;.","0.018;.;0.019;0.028","0.723;.;0.75;0.743",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","417,1","0.0024","418","0/1","65,141","0.6845","206",null,"chr12:106711491:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.669"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RGS22","chr8:100008447","RGS22(E763D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits thereby driving them into their inactive GDP-bound form. {ECO:0000250}.; ",{"$nulls":4},"p.Glu763Asp","c.2289G>T","MODERATE","763/1264",15,{"$nulls":5},"5","275","267","199","189","251","236","0","0","0","0.1907",{"$nulls":20},"2.604591","1.48;.;1.48;1.48;1.48","2.36;.;.;.;.","0.548388","-2.16;.;-2.16;-2.16;-2.3","1.0;.;1.0;.;.","0.019;.;0.024;0.019;0.0","0.486;0.39;0.497;0.443;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","261,0","0","261","0/1","206,44","0.176","250",null,"chr8:100008447:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1693"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RHPN1","chr8:143375582","RHPN1(C30W)",null,null,"domain (REM-1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Has no enzymatic activity. May serve as a target for Rho, and interact with some cytoskeletal component upon Rho binding or relay a Rho signal to other molecules. {ECO:0000250|UniProtKB:Q61085}.; ",{"$nulls":4},"p.Cys30Trp","c.90C>G","MODERATE","30/670",2,{"$nulls":5},"5","71","71","58","59","33","35","0","0","0","0.2857",{"$nulls":20},"0.290288","1.58",null,"0.998206","-1.07",null,"0.004","0.375",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","69,0","0","69","0/1","59,11","0.1571","70",null,"chr8:143375582:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1695"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RING1","chr6:33210093","RING1(S140R)",null,null,"region of interest (Necessary for transcriptional repression ), modified residue (Phosphoserine)","modified-residue:Phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Constitutes one of the E3 ubiquitin-protein ligases that mediate monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. Compared to RNF2/RING2, it does not have the main E3 ubiquitin ligase activity on histone H2A, and it may rather act as a modulator of RNF2/RING2 activity. {ECO:0000269|PubMed:16359901}.; ",{"$nulls":4},"p.Ser140Arg","c.418A>C","MODERATE","140/406",4,{"$nulls":5},"4","383","224","268","173","354","213","0","0","0","0.0516",{"$nulls":20},"4.178556","-1.16","2.625","0.999992","-4.79","1.0","0.001","0.827",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","386,0","0","386","0/1","212,12","0.0536","224",null,"chr6:33210093:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.052"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RPA1","chr17:1875780","RPA1(P192T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: As part of the heterotrimeric replication protein A complex (RPA/RP-A), binds and stabilizes single-stranded DNA intermediates, that form during DNA replication or upon DNA stress. It prevents their reannealing and in parallel, recruits and activates different proteins and complexes involved in DNA metabolism (PubMed:27723720, PubMed:27723717). Thereby, it plays an essential role both in DNA replication and the cellular response to DNA damage (PubMed:9430682). In the cellular response to DNA damage, the RPA complex controls DNA repair and DNA damage checkpoint activation. Through recruitment of ATRIP activates the ATR kinase a master regulator of the DNA damage response (PubMed:24332808). It is required for the recruitment of the DNA double-strand break repair factors RAD51 and RAD52 to chromatin in response to DNA damage (PubMed:17765923). Also recruits to sites of DNA damage proteins like XPA and XPG that are involved in nucleotide excision repair and is required for this mechanism of DNA repair (PubMed:7697716). Plays also a role in base excision repair (BER) probably through interaction with UNG (PubMed:9765279). Also recruits SMARCAL1/HARP, which is involved in replication fork restart, to sites of DNA damage. May also play a role in telomere maintenance (PubMed:17959650). As part of the alternative replication protein A complex, aRPA, binds single- stranded DNA and probably plays a role in DNA repair. Compared to the RPA2-containing, canonical RPA complex, may not support chromosomal DNA replication and cell cycle progression through S- phase. The aRPA may not promote efficient priming by DNA polymerase alpha but could support DNA synthesis by polymerase delta in presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange (PubMed:19996105). {ECO:0000269|PubMed:12791985, ECO:0000269|PubMed:17765923, ECO:0000269|PubMed:17959650, ECO:0000269|PubMed:19116208, ECO:0000269|PubMed:19996105, ECO:0000269|PubMed:24332808, ECO:0000269|PubMed:27723717, ECO:0000269|PubMed:27723720, ECO:0000269|PubMed:7697716, ECO:0000269|PubMed:7700386, ECO:0000269|PubMed:9430682, ECO:0000269|PubMed:9765279}.; ","level2",{"$nulls":3},"p.Pro192Thr","c.574C>A","MODERATE","192/616",7,{"$nulls":5},"5","182","239","124","156","164","221","0","0","0","0.1086",{"$nulls":20},"3.80369","0.48","2.865","1","-7.55","1.0",null,"0.873",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kDNA_REPLICATION,kHOMOLOGOUS_RECOMBINATION,kMISMATCH_REPAIR",{"$nulls":3},"0/0","180,0","0","180","0/1","204,30","0.1282","234",null,"chr17:1875780:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1282"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RPS29","chr14:49586343","RPS29(G2C)",{"$nulls":6},255,"PASS","Missense","rs759810229",0.0001512,"DISEASE: Diamond-Blackfan anemia 13 (DBA13) [MIM:615909]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:24829207}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ",{"$nulls":5},"p.Gly2Cys","c.4G>T","MODERATE","2/67",1,1,{"$nulls":4},"5","286","286","220","231","255","245","0","0","0","0.1224",{"$nulls":20},"4.014797",null,null,"1","-6.91;-7.3;.;.",".;1.0;1.0;.","0.001;0.001;.;.","0.881;0.869;.;.",{"$nulls":3},"ExAC_FIN_AF",0.0001512,"AD","Diamond-Blackfan anemia 13","Cardiovascular; Hematologic; Oncologic",{"$nulls":3},"C4014641","0/0","286,0","0","286","0/1","241,36","0.13","277",null,"chr14:49586343:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1255"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RPS6KC1","chr1:213240888","RPS6KC1(P471L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transmitting sphingosine-1 phosphate (SPP)-mediated signaling into the cell (PubMed:12077123). Plays a role in the recruitment of PRDX3 to early endosomes (PubMed:15750338). {ECO:0000269|PubMed:12077123, ECO:0000269|PubMed:15750338}.; ",{"$nulls":4},"p.Pro471Leu","c.1412C>T","MODERATE","471/1066",11,{"$nulls":5},"5","288","130","228","105","244","117","0","0","0","0.2991",{"$nulls":20},"2.69996",".;1.39;.;.;1.42;1.42",".;.;.;.;2.2;.","0.999329",".;-4.42;.;.;-4.42;-4.42",".;0.967;.;0.967;0.098;.",".;0.001;.;.;0.005;0.005","0.484;0.427;0.506;0.548;0.567;0.402",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","282,0","0","282","0/1","89,37","0.2937","126",null,"chr1:213240888:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3333"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RTL1","chr14:100882633","RTL1(Q713fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta. {ECO:0000250}.; ",{"$nulls":4},"p.Gln713fs","c.2139_2155delGAACGTGATTCACTTCA","HIGH","713/1358",1,{"$nulls":5},"5","482","414","402","340","423","358","0","0","0","0.2123",{"$nulls":5},"(RTL1|ENSG00000254656|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009].  ",null,null,"0/0","552,0","0","552","0/1","343,87","0.2023","430",null,"chr14:100882633:ATGAAGTGAATCACGTTC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2206"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RUFY3","chr4:70773551","RUFY3(N246T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a role in the generation of neuronal polarity formation and axon growth (By similarity). Implicated in the formation of a single axon by developing neurons (By similarity). May inhibit the formation of additional axons by inhibition of PI3K in minor neuronal processes (By similarity). Plays a role in the formation of F-actin-enriched protrusive structures at the cell periphery (PubMed:25766321). Plays a role in cytoskeletal organization by regulating the subcellular localization of FSCN1 and DBN1 at axonal growth cones (By similarity). Promotes gastric cancer cell migration and invasion in a PAK1-dependent manner (PubMed:25766321). {ECO:0000250|UniProtKB:Q5FVJ0, ECO:0000250|UniProtKB:Q9D394, ECO:0000269|PubMed:25766321}.; ",{"$nulls":4},"p.Asn246Thr","c.737A>C","MODERATE","246/620",6,{"$nulls":5},"3",null,null,"105","162",{"$nulls":26},"2.345027","2.55;2.98;2.58;1.84;2.97",".;1.79;1.79;.;.","0.998794;0.999599;0.999599;0.999759;0.999599","-2.99;-2.86;-2.84;-2.57;-2.64","0.014;0.029;0.0;.;.","0.041;0.021;0.023;0.028;0.031","0.198;0.188;0.189;.;0.195",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","146,1","0.0068","147","0/1","209,12","0.0543","221",null,"chr4:70773551:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0556"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RUNDC3A","chr17:44315004","RUNDC3A(Q209*)",null,null,"region of interest (Interaction with RAP2A )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May act as an effector of RAP2A in neuronal cells. {ECO:0000250}.; ",{"$nulls":4},"p.Gln209*","c.624_625delGCinsCT","HIGH","208/446",6,{"$nulls":5},"4","177","171",null,null,"136","143","0","0","0","0.3077",{"$nulls":5},"(RUNDC3A|ENSG00000108309|1|1.00)","(RUNDC3A|ENSG00000108309|1|1.00)",{"$nulls":24},"Unknown",-1,{"$nulls":7},"0|0","183,0","0","183","0|1","126,60","0.3226","186",null,"chr17:44315004:GC:CT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RUNDC3A","chr17:44315004","RUNDC3A(Q209*)",null,null,"region of interest (Interaction with RAP2A )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May act as an effector of RAP2A in neuronal cells. {ECO:0000250}.; ",{"$nulls":4},"p.Gln209*","c.624_625delGCinsCT","HIGH","208/446",6,{"$nulls":5},"4","177","91",null,null,"136","79","0","0","0","0.6835",{"$nulls":5},"(RUNDC3A|ENSG00000108309|1|1.00)","(RUNDC3A|ENSG00000108309|1|1.00)",{"$nulls":24},"Unknown",-1,{"$nulls":7},"0|0","183,0","0","183","0|1","34,80","0.7018","114",null,"chr17:44315004:GC:CT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RYR2","chr1:237634973","RYR2(R2258H)",{"$nulls":6},255,"PASS","Missense","rs779289104",8.275e-06,"DISEASE: Arrhythmogenic right ventricular dysplasia, familial, 2 (ARVD2) [MIM:600996]: A congenital heart disease characterized by infiltration of adipose and fibrous tissue into the right ventricle and loss of myocardial cells, resulting in ventricular and supraventricular arrhythmias. {ECO:0000269|PubMed:11159936}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ventricular tachycardia, catecholaminergic polymorphic, 1, with or without atrial dysfunction and/or dilated cardiomyopathy (CPVT1) [MIM:604772]: An arrhythmogenic disorder characterized by stress-induced, bidirectional ventricular tachycardia that may degenerate into cardiac arrest and cause sudden death. Patients present with recurrent syncope, seizures, or sudden death after physical activity or emotional stress. CPVT1 inheritance is autosomal dominant. {ECO:0000269|PubMed:11157710, ECO:0000269|PubMed:11208676, ECO:0000269|PubMed:12093772, ECO:0000269|PubMed:12106942, ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:15046072, ECO:0000269|PubMed:15046073, ECO:0000269|PubMed:15466642, ECO:0000269|PubMed:15544015, ECO:0000269|PubMed:16188589, ECO:0000269|PubMed:17984046, ECO:0000269|PubMed:24793461, ECO:0000269|PubMed:25372681, ECO:0000269|PubMed:27733687}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering cardiac muscle contraction. Aberrant channel activation can lead to cardiac arrhythmia. In cardiac myocytes, calcium release is triggered by increased Ca(2+) levels due to activation of the L-type calcium channel CACNA1C. The calcium channel activity is modulated by formation of heterotetramers with RYR3. Required for cellular calcium ion homeostasis. Required for embryonic heart development. {ECO:0000269|PubMed:10830164, ECO:0000269|PubMed:20056922, ECO:0000269|PubMed:27733687}.; ","acmg",{"$nulls":3},"p.Arg2258His","c.6773G>A","MODERATE","2258/4967",44,1,{"$nulls":4},"5","434","525","288","351","387","460","0","0","0","0.0957",{"$nulls":20},"4.259814","-3.75;.","1.445;.","0.876823","-2.04;.","0.999;.","0.004;.","0.51;.",{"$nulls":3},"ExAC_AF",8.275e-06,"AD","Ventricular tachycardia, catecholaminergic polymorphic, 1; Arrhythmogenic right ventricular dysplasia 2  ","Cardiovascular",null,"This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008].  ",null,"C1832931| C4053736","0/0","422,0","0","422","0/1","430,49","0.1023","479",null,"chr1:237634973:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0997"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RYR2","chr1:237634973","RYR2(R2258H)",{"$nulls":6},255,"PASS","Missense","rs779289104",8.275e-06,"DISEASE: Arrhythmogenic right ventricular dysplasia, familial, 2 (ARVD2) [MIM:600996]: A congenital heart disease characterized by infiltration of adipose and fibrous tissue into the right ventricle and loss of myocardial cells, resulting in ventricular and supraventricular arrhythmias. {ECO:0000269|PubMed:11159936}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ventricular tachycardia, catecholaminergic polymorphic, 1, with or without atrial dysfunction and/or dilated cardiomyopathy (CPVT1) [MIM:604772]: An arrhythmogenic disorder characterized by stress-induced, bidirectional ventricular tachycardia that may degenerate into cardiac arrest and cause sudden death. Patients present with recurrent syncope, seizures, or sudden death after physical activity or emotional stress. CPVT1 inheritance is autosomal dominant. {ECO:0000269|PubMed:11157710, ECO:0000269|PubMed:11208676, ECO:0000269|PubMed:12093772, ECO:0000269|PubMed:12106942, ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:15046072, ECO:0000269|PubMed:15046073, ECO:0000269|PubMed:15466642, ECO:0000269|PubMed:15544015, ECO:0000269|PubMed:16188589, ECO:0000269|PubMed:17984046, ECO:0000269|PubMed:24793461, ECO:0000269|PubMed:25372681, ECO:0000269|PubMed:27733687}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering cardiac muscle contraction. Aberrant channel activation can lead to cardiac arrhythmia. In cardiac myocytes, calcium release is triggered by increased Ca(2+) levels due to activation of the L-type calcium channel CACNA1C. The calcium channel activity is modulated by formation of heterotetramers with RYR3. Required for cellular calcium ion homeostasis. Required for embryonic heart development. {ECO:0000269|PubMed:10830164, ECO:0000269|PubMed:20056922, ECO:0000269|PubMed:27733687}.; ","acmg",{"$nulls":3},"p.Arg2258His","c.6773G>A","MODERATE","2258/4967",44,1,{"$nulls":4},"5","434","557","288","372","388","481","0","0","0","0.3867",{"$nulls":20},"4.259814","-3.75;.","1.445;.","0.876823","-2.04;.","0.999;.","0.004;.","0.51;.",{"$nulls":3},"ExAC_AF",8.275e-06,"AD","Ventricular tachycardia, catecholaminergic polymorphic, 1; Arrhythmogenic right ventricular dysplasia 2  ","Cardiovascular",null,"This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008].  ",null,"C1832931| C4053736","0/0","422,0","0","422","0/1","319,212","0.3992","531",null,"chr1:237634973:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3817"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","RYR3","chr15:33742397","RYR3(V2618L)",null,null,"topological domain (Cytoplasmic ), repeat (3 ), region of interest (4 X approximate repeats ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm in muscle and thereby plays a role in triggering muscle contraction. May regulate Ca(2+) release by other calcium channels. Calcium channel that mediates Ca(2+)-induced Ca(2+) release from the endoplasmic reticulum in non-muscle cells. Contributes to cellular calcium ion homeostasis (By similarity). Plays a role in cellular calcium signaling. {ECO:0000250, ECO:0000269|PubMed:12354756}.; ",{"$nulls":4},"p.Val2618Leu","c.7852G>C","MODERATE","2618/4873",52,{"$nulls":5},"5","452","496","321","347","376","412","0","0","0","0.1044",{"$nulls":20},"3.409089",".;-3.0;.;.;.","1.665;1.665;.;.;.","0.969185",".;-1.87;.;.;.","0.239;0.03;.;.;.",".;0.007;.;.;.","0.367;0.489;0.485;0.495;0.482",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","443,0","0","443","0/1","426,55","0.1143","481",null,"chr15:33742397:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1239"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","RYR3","chr15:33742397","RYR3(V2618L)",null,null,"topological domain (Cytoplasmic ), repeat (3 ), region of interest (4 X approximate repeats ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm in muscle and thereby plays a role in triggering muscle contraction. May regulate Ca(2+) release by other calcium channels. Calcium channel that mediates Ca(2+)-induced Ca(2+) release from the endoplasmic reticulum in non-muscle cells. Contributes to cellular calcium ion homeostasis (By similarity). Plays a role in cellular calcium signaling. {ECO:0000250, ECO:0000269|PubMed:12354756}.; ",{"$nulls":4},"p.Val2618Leu","c.7852G>C","MODERATE","2618/4873",52,{"$nulls":5},"5","452","224","321","158","376","184","0","0","0","0.288",{"$nulls":20},"3.409089",".;-3.0;.;.;.","1.665;1.665;.;.;.","0.969185",".;-1.87;.;.;.","0.239;0.03;.;.;.",".;0.007;.;.;.","0.367;0.489;0.485;0.495;0.482",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","443,0","0","443","0/1","154,63","0.2903","217",null,"chr15:33742397:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2785"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SCAMP2","chr15:74850615","SCAMP2(N177K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.; ",{"$nulls":4},"p.Asn177Lys","c.531C>A","MODERATE","177/329",6,{"$nulls":5},"5","300","363","209","248","264","316","0","0","0","0.2595",{"$nulls":20},"0.64815","2.35","0.205;.;.;.;.","1","-1.5;-1.59;-1.84;-1.33;-1.27","0.0;.;.;.;.","0.111;0.09;0.271;0.081;0.109","0.139;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","296,0","0","296","0/1","256,97","0.2748","353",null,"chr15:74850615:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2782"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SCAMP2","chr15:74850615","SCAMP2(N177K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.; ",{"$nulls":4},"p.Asn177Lys","c.531C>A","MODERATE","177/329",6,{"$nulls":5},"5","300","195","209","132","264","177","0","0","0","0.5028",{"$nulls":20},"0.64815","2.35","0.205;.;.;.;.","1","-1.5;-1.59;-1.84;-1.33;-1.27","0.0;.;.;.;.","0.111;0.09;0.271;0.081;0.109","0.139;.;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","290,0","0","290","0/1","92,86","0.4831","178",null,"chr15:74850615:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4697"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SCN8A","chr12:51765702","SCN8A(P870H)",null,null,"topological domain (Cytoplasmic ), repeat (II )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Cognitive impairment with or without cerebellar ataxia (CIAT) [MIM:614306]: A disorder characterized by markedly delayed cognitive and motor development, attention deficit disorder, and cerebellar ataxia. Features include bilateral esophoria, strabismatic amblyopia, unsustained gaze evoked nystagmus on horizontal gaze, ataxic gait, dysmetria in the upper limbs and dysarthria, with normal strength, tone, and reflexes. {ECO:0000269|PubMed:16236810}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 13 (EIEE13) [MIM:614558]: A form of epilepsy characterized by frequent tonic seizures or spasms beginning in infancy with a specific EEG finding of suppression-burst patterns, characterized by high- voltage bursts alternating with almost flat suppression phases. Patients may progress to West syndrome, which is characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on EEG. EIEE13 is a severe form consisting of early-onset seizures, features of autism, intellectual disability, ataxia, and sudden unexplained death in epilepsy. {ECO:0000269|PubMed:22365152, ECO:0000269|PubMed:23708187, ECO:0000269|PubMed:24352161, ECO:0000269|PubMed:24874546, ECO:0000269|PubMed:24888894, ECO:0000269|PubMed:25239001, ECO:0000269|PubMed:25568300, ECO:0000269|PubMed:25725044, ECO:0000269|PubMed:25785782, ECO:0000269|PubMed:25818041, ECO:0000269|PubMed:26900580, ECO:0000269|PubMed:26993267, ECO:0000269|PubMed:27210545, ECO:0000269|PubMed:27864847, ECO:0000269|PubMed:28923014}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Seizures, benign familial infantile, 5 (BFIS5) [MIM:617080]: A form of benign familial infantile epilepsy, a neurologic disorder characterized by afebrile seizures occurring in clusters during the first year of life, without neurologic sequelae. BFIS5 inheritance is autosomal dominant. {ECO:0000269|PubMed:26677014, ECO:0000269|PubMed:27210545}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. In macrophages and melanoma cells, isoform 5 may participate in the control of podosome and invadopodia formation. {ECO:0000269|PubMed:19136557}.; ",{"$nulls":4},"p.Pro870His","c.2609C>A","MODERATE","870/1991",15,{"$nulls":5},"3","162","267",{"$nulls":4},"0.0063","0.0063",{"$nulls":22},"3.805153","-5.13;-5.13;-5.13;.;.","3.27;3.27;3.27;.;3.27","1","-8.71;-8.71;-8.39;.;.","1.0;.;.;.;.","0.0;0.0;0.0;.;.","0.786;0.772;0.791;0.785;0.774",{"$nulls":3},"Unknown",-1,"AD","Cognitive impairment with or without cerebellar ataxia; Epileptic encephalopathy, early infantile, 13","Neurologic; Ophthalmologic",{"$nulls":3},"C3281191| C5193056| C4310728| C3280415","0/0","158,1","0.0063","159","0/1","240,22","0.084","262",null,"chr12:51765702:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SCYL2","chr12:100323618","SCYL2(L501V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of AP2-containing clathrin coated structures at the plasma membrane or of endocytic coated vesicles. According to PubMed:15809293, probable serine/threonine-protein kinase that phosphorylates, in vitro, the beta2-subunit of the plasma membrane adapter complex AP2 and other proteins in presence of poly-L- lysine. According to PubMed:16914521, has no detectable kinase activity in vitro. May regulate clathrin-dependent trafficking between the TGN and/or the endosomal system. {ECO:0000269|PubMed:15809293, ECO:0000269|PubMed:16914521}.; ",{"$nulls":4},"p.Leu501Val","c.1501C>G","MODERATE","501/933",12,{"$nulls":5},"5","393","347","261","222","367","317","0","0","0","0.2713",{"$nulls":20},"2.772531","1.46;.;1.46",".;.;1.6","0.999996","-1.62;.;-1.52",".;.;0.64","0.099;.;0.101",".;0.692;0.705",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5231494","0/0","365,0","0","365","0/1","238,92","0.2788","330",null,"chr12:100323618:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2703"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SCYL2","chr12:100323618","SCYL2(L501V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of AP2-containing clathrin coated structures at the plasma membrane or of endocytic coated vesicles. According to PubMed:15809293, probable serine/threonine-protein kinase that phosphorylates, in vitro, the beta2-subunit of the plasma membrane adapter complex AP2 and other proteins in presence of poly-L- lysine. According to PubMed:16914521, has no detectable kinase activity in vitro. May regulate clathrin-dependent trafficking between the TGN and/or the endosomal system. {ECO:0000269|PubMed:15809293, ECO:0000269|PubMed:16914521}.; ",{"$nulls":4},"p.Leu501Val","c.1501C>G","MODERATE","501/933",12,{"$nulls":5},"5","393","161","261","102","363","144","0","0","0","0.6389",{"$nulls":20},"2.772531","1.46;.;1.46",".;.;1.6","0.999996","-1.62;.;-1.52",".;.;0.64","0.099;.;0.101",".;0.692;0.705",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C5231494","0/0","383,0","0","383","0/1","59,97","0.6218","156",null,"chr12:100323618:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6275"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SERINC1","chr6:122452010","SERINC1(L210fs)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Enhances the incorporation of serine into phosphatidylserine and sphingolipids. {ECO:0000250|UniProtKB:Q7TNK0}.; ",{"$nulls":4},"p.Leu210fs","c.624_636delGTCTTTAGTTGCT","HIGH","208/453",6,{"$nulls":5},"5","214","328","158","227","170","240","0","0","0","0.2458",{"$nulls":5},"(SERINC1|ENSG00000111897|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","212,0","0","212","0/1","234,72","0.2353","306",null,"chr6:122452010:TAGCAACTAAAGAC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2247"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SERINC1","chr6:122452010","SERINC1(L210fs)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Enhances the incorporation of serine into phosphatidylserine and sphingolipids. {ECO:0000250|UniProtKB:Q7TNK0}.; ",{"$nulls":4},"p.Leu210fs","c.624_636delGTCTTTAGTTGCT","HIGH","208/453",6,{"$nulls":5},"5","214","297","158","213","171","228","0","0","0","0.1711",{"$nulls":5},"(SERINC1|ENSG00000111897|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","212,0","0","212","0/1","239,43","0.1525","282",null,"chr6:122452010:TAGCAACTAAAGAC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1643"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SETDB1","chr1:150929998","SETDB1(D98H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). {ECO:0000269|PubMed:12869583, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.; ","gedi",{"$nulls":3},"p.Asp98His","c.292G>C","MODERATE","98/1291",3,{"$nulls":5},"5","431","490","322","342","375","408","0","0","0","0.2475",{"$nulls":20},"3.919683",".;-2.43;.;0.77;1.34;-2.43;.;1.05;.",".;1.59;.;1.59;.;1.59;.;.;.","0.937098;0.577145;0.577145;0.577145","-3.59;-1.63;-3.52;-1.94;-1.74;-1.63;-3.15;-1.63;-3.79",".;0.989;.;0.969;0.969;0.997;.;0.976;.","0.029;0.02;0.018;0.039;0.027;0.02;0.017;0.009;0.018",".;0.382;.;0.317;.;0.4;0.375;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","414,0","0","414","0/1","322,113","0.2598","435",null,"chr1:150929998:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2544"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SETDB1","chr1:150929998","SETDB1(D98H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. H3 'Lys-9' trimethylation is coordinated with DNA methylation. Probably forms a complex with MBD1 and ATF7IP that represses transcription and couples DNA methylation and histone 'Lys-9' trimethylation. Its activity is dependent on MBD1 and is heritably maintained through DNA replication by being recruited by CAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factor recruited by KRAB zinc-finger proteins. Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). {ECO:0000269|PubMed:12869583, ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775, ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306, ECO:0000269|PubMed:27029610}.; ","gedi",{"$nulls":3},"p.Asp98His","c.292G>C","MODERATE","98/1291",3,{"$nulls":5},"5","431","328","322","236","374","261","0","0","0","0.5249",{"$nulls":20},"3.919683",".;-2.43;.;0.77;1.34;-2.43;.;1.05;.",".;1.59;.;1.59;.;1.59;.;.;.","0.937098;0.577145;0.577145;0.577145","-3.59;-1.63;-3.52;-1.94;-1.74;-1.63;-3.15;-1.63;-3.79",".;0.989;.;0.969;0.969;0.997;.;0.976;.","0.029;0.02;0.018;0.039;0.027;0.02;0.017;0.009;0.018",".;0.382;.;0.317;.;0.4;0.375;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","414,0","0","414","0/1","147,155","0.5132","302",null,"chr1:150929998:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5042"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SF3B1","chr2:197408582","SF3B1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077). {ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643}.; ","gedi|foundationOne",{"$nulls":4},"c.905-1G>C","HIGH",null,7,{"$nulls":5},"5","113","156","86","115","102","138","0","0","0","0.2246",{"$nulls":5},"(SF3B1|ENSG00000115524|1|1.00)",{"$nulls":14},"5.621418",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":6},"C3463824","0/0","112,0","0","112","0/1","116,38","0.2468","154",null,"chr2:197408582:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2261"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SF3B1","chr2:197408582","SF3B1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex (PubMed:27720643). SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (PubMed:12234937). May also be involved in the assembly of the 'E' complex (PubMed:10882114). Belongs also to the minor U12-dependent spliceosome, which is involved in the splicing of rare class of nuclear pre-mRNA intron (PubMed:15146077). {ECO:0000269|PubMed:10882114, ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:27720643}.; ","gedi|foundationOne",{"$nulls":4},"c.905-1G>C","HIGH",null,7,{"$nulls":5},"5","113","89","86","69","101","84","0","0","0","0.2857",{"$nulls":5},"(SF3B1|ENSG00000115524|1|1.00)",{"$nulls":14},"5.621418",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":6},"C3463824","0/0","112,0","0","112","0/1","65,24","0.2697","89",null,"chr2:197408582:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2609"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SHISA9","chr16:13203523","SHISA9(N274S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulator of short-term neuronal synaptic plasticity in the dentate gyrus. Associates with AMPA receptors (ionotropic glutamate receptors) in synaptic spines and promotes AMPA receptor desensitization at excitatory synapses (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asn274Ser","c.821A>G","MODERATE","274/424",3,{"$nulls":5},"4","289","325","193","227","245","267","0","0","0","0.367",{"$nulls":20},"2.155724",null,"1.09","0.899239",null,"0.615",null,"0.388",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","276,0","0","276","0/1","201,109","0.3516","310",null,"chr16:13203523:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3524"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SHISA9","chr16:13203523","SHISA9(N274S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulator of short-term neuronal synaptic plasticity in the dentate gyrus. Associates with AMPA receptors (ionotropic glutamate receptors) in synaptic spines and promotes AMPA receptor desensitization at excitatory synapses (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asn274Ser","c.821A>G","MODERATE","274/424",3,{"$nulls":5},"4","289","210","193","131","244","165","0","0","0","0.7394",{"$nulls":20},"2.155724",null,"1.09","0.899239",null,"0.615",null,"0.388",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","276,0","0","276","0/1","49,150","0.7538","199",null,"chr16:13203523:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7405"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC11A2","chr12:50996949","SLC11A2(Q262H)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Anemia, hypochromic microcytic, with iron overload 1 (AHMIO1) [MIM:206100]: A hematologic disease characterized by abnormal hemoglobin content in the erythrocytes which are reduced in size. The disorder is due to an error of iron metabolism that results in high serum iron, massive hepatic iron deposition, and absence of sideroblasts and stainable bone marrow iron store. Despite adequate transferrin-iron complex, delivery of iron to the erythroid bone marrow is apparently insufficient for the demands of hemoglobin synthesis. {ECO:0000269|PubMed:15459009, ECO:0000269|PubMed:16160008, ECO:0000269|PubMed:16439678}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Important in metal transport, in particular iron. Can also transport manganese, cobalt, cadmium, nickel, vanadium and lead. Involved in apical iron uptake into duodenal enterocytes. Involved in iron transport from acidified endosomes into the cytoplasm of erythroid precursor cells. May play an important role in hepatic iron accumulation and tissue iron distribution. May serve to import iron into the mitochondria. {ECO:0000269|PubMed:17109629, ECO:0000269|PubMed:24448823, ECO:0000269|PubMed:25326704, ECO:0000269|PubMed:25491917}.; ",{"$nulls":4},"p.Gln262His","c.786G>C","MODERATE","262/590",9,{"$nulls":5},"4","524","521","377","343","479","462","0","0","0","0.1905",{"$nulls":20},"3.518239","-0.43;.;.;-0.43;-0.43;.;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43","3.37;3.37;.;3.37;3.37;3.37;.;3.37;.;.;.;.","0.999892;0.999892;0.999892;0.999939;0.999892;0.999939;0.999892;0.999939","-4.87;.;.;-4.87;-4.87;.;-4.87;-4.87;-4.87;-4.78;-4.87;-4.92","0.999;0.999;.;0.999;1.0;1.0;1.0;1.0;.;.;1.0;.","0.016;.;.;0.016;0.022;.;0.016;0.022;0.022;0.033;0.016;0.021","0.886;.;.;0.886;0.884;.;0.878;0.885;0.881;0.884;0.857;.",{"$nulls":3},"Unknown",-1,"AR","Anemia, hypochromic microcytic, with iron overload","Hematologic",{"$nulls":3},"C3806153","0/0","517,0","0","517","0/1","409,89","0.1787","498",null,"chr12:50996949:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.172"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC12A4","chr16:67968475","SLC12A4(W60C)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 7. )",{"$nulls":3},255,"PASS","Missense","rs1274574568",-1,null,"FUNCTION: Mediates electroneutral potassium-chloride cotransport when activated by cell swelling. May contribute to cell volume homeostasis in single cells. May be involved in the regulation of basolateral Cl(-) exit in NaCl absorbing epithelia (By similarity). Isoform 4 has no transport activity. {ECO:0000250}.; ",{"$nulls":4},"p.Trp60Cys","c.180G>T","MODERATE","60/1087",1,{"$nulls":5},"5","477","306","346","226","345","214","0","0","0","0.1495",{"$nulls":20},"4.419881","-1.93","0","1;0.961234;1;0.961234;1","-0.7;.","0.947;0.822","0.022;.","0.731;0.747",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","449,0","0","449","0/1","236,40","0.1449","276",null,"chr16:67968475:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1372"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC15A4","chr12:128823399","SLC15A4(Q182L)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Proton oligopeptide cotransporter. Transports free histidine and certain di- and tripeptides. {ECO:0000269|PubMed:16289537}.; ",{"$nulls":4},"p.Gln182Leu","c.545A>T","MODERATE","182/577",1,{"$nulls":5},"5","103","84","88","78","79","64","0","0","0","0.2812",{"$nulls":20},"4.917328","2.82","3.94","0.999995","-6.08","0.988","0.019","0.826",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","101,0","0","101","0/1","65,19","0.2262","84",null,"chr12:128823399:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2308"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC15A4","chr12:128823399","SLC15A4(Q182L)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Proton oligopeptide cotransporter. Transports free histidine and certain di- and tripeptides. {ECO:0000269|PubMed:16289537}.; ",{"$nulls":4},"p.Gln182Leu","c.545A>T","MODERATE","182/577",1,{"$nulls":5},"5","103","91","88","75","79","65","0","0","0","0.3385",{"$nulls":20},"4.917328","2.82","3.94","0.999995","-6.08","0.988","0.019","0.826",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","101,0","0","101","0/1","64,26","0.2889","90",null,"chr12:128823399:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2933"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC16A8","chr22:38078492","SLC16A8(E471*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Proton-linked monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu471*","c.1411G>T","HIGH","471/504",5,{"$nulls":5},"5","302","432","236","340","253","369","0","0","0","0.0949",{"$nulls":20},"6.03156",null,null,"0.97889",{"$nulls":3},"0.043",{"$nulls":3},"Unknown",-1,{"$nulls":4},"SLC16A8 is a member of a family of proton-coupled monocarboxylate transporters that mediate lactate transport across cell membranes (Yoon et al., 1999 [PubMed 10493836]).[supplied by OMIM, Apr 2010].  ",null,null,"0/0","296,0","0","296","0/1","388,37","0.0871","425",null,"chr22:38078492:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0971"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC16A8","chr22:38078492","SLC16A8(E471*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Proton-linked monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu471*","c.1411G>T","HIGH","471/504",5,{"$nulls":5},"5","302","368","236","284","253","307","0","0","0","0.1466",{"$nulls":20},"6.03156",null,null,"0.97889",{"$nulls":3},"0.043",{"$nulls":3},"Unknown",-1,{"$nulls":4},"SLC16A8 is a member of a family of proton-coupled monocarboxylate transporters that mediate lactate transport across cell membranes (Yoon et al., 1999 [PubMed 10493836]).[supplied by OMIM, Apr 2010].  ",null,null,"0/0","296,0","0","296","0/1","314,48","0.1326","362",null,"chr22:38078492:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1408"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC17A8","chr12:100412785","SLC17A8(A401G)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells. May also mediate the transport of inorganic phosphate. {ECO:0000269|PubMed:12151341}.; ",{"$nulls":4},"p.Ala401Gly","c.1202C>G","MODERATE","401/589",10,{"$nulls":5},"5","636","359","503","281","522","304","0","0","0","0.3092",{"$nulls":20},"2.906543","0.14","1.77;.","1","-3.75","0.402;0.344","0.142;0.158","0.704;0.691",{"$nulls":3},"Unknown",-1,"AD","Deafness, autosomal dominant 25","Audiologic/Otolaryngologic",{"$nulls":3},"C1854158","0/0","626,0","0","626","0/1","242,106","0.3046","348",null,"chr12:100412785:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3238"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC22A23","chr6:3410189","SLC22A23(L304F)",null,null,"transmembrane region (Helical ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu304Phe","c.912A>T","MODERATE","304/694",3,{"$nulls":5},"5","252","280","212","219","207","236","0","0","0","0.1822",{"$nulls":20},"3.662156","-0.81",".;2.225;.;.;.;.;2.225","0.998849;0.997424;0.997424;0.998849;0.998849","-1.81;-1.81;-1.64;-1.64;-1.99;-1.86;-2.86","0.999;0.996;.;.;.;.;.","0.024;0.025;0.034;0.034;0.014;0.027;0.006","0.681;0.681;0.665;0.662;.;.;0.646",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","244,0","0","244","0/1","215,45","0.1731","260",null,"chr6:3410189:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1689"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC25A6","chrX:1387379","SLC25A6(S213R)",null,null,"transmembrane region (Helical; Name=5 ), repeat (Solcar 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis. {ECO:0000269|PubMed:15033708}.; ","mitocarta",{"$nulls":3},"p.Ser213Arg","c.639C>A","MODERATE","213/298",3,{"$nulls":5},"4","1886","2203","1313","1469","1682","1945","0","0","0","0.1974",{"$nulls":20},"2.441386","-1.32",null,"1","-3.14","0.978","0.044","0.654",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein is implicated in the function of the permability transition pore complex (PTPC), which regulates the release of mitochondrial products that induce apoptosis. The human genome contains several non-transcribed pseudogenes of this gene. [provided by RefSeq, Jun 2013].  ",null,null,"0/0","1663,0","0","1663","0/1","1506,367","0.1959","1873",null,"chrX:1387379:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1831"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC25A6","chrX:1387379","SLC25A6(S213R)",null,null,"transmembrane region (Helical; Name=5 ), repeat (Solcar 3 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the exchange of cytoplasmic ADP with mitochondrial ATP across the mitochondrial inner membrane. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis. {ECO:0000269|PubMed:15033708}.; ","mitocarta",{"$nulls":3},"p.Ser213Arg","c.639C>A","MODERATE","213/298",3,{"$nulls":5},"4","1886","1793","1313","1201","1677","1586","0","0","0","0.1614",{"$nulls":20},"2.441386","-1.32",null,"1","-3.14","0.978","0.044","0.654",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein is implicated in the function of the permability transition pore complex (PTPC), which regulates the release of mitochondrial products that induce apoptosis. The human genome contains several non-transcribed pseudogenes of this gene. [provided by RefSeq, Jun 2013].  ",null,null,"0/0","1688,0","0","1688","0/1","1308,241","0.1556","1549",null,"chrX:1387379:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1499"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC26A9","chr1:205914894","SLC26A9(R886_T887del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: DIDS- and thiosulfate- sensitive anion exchanger mediating chloride, sulfate and oxalate transport. Mediates chloride/bicarbonate exchange or chloride-independent bicarbonate extrusion thus assuring bicarbonate secretion. Inhibited by ammonium and thiosulfate. {ECO:0000269|PubMed:11834742, ECO:0000269|PubMed:15800055}.; ",{"$nulls":4},"p.Arg886_Thr887del","c.2656_2661delCGGACA","MODERATE","886/887",21,{"$nulls":5},"5","406","460","374","382","372","400","0","0","0","0.1225",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","445,0","0","445","0/1","407,68","0.1432","475",null,"chr1:205914894:ATGTCCG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1545"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC2A6","chr9:133473538","SLC2A6(L367V)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Facilitative glucose transporter; binds cytochalasin B with low affinity.; ",{"$nulls":4},"p.Leu367Val","c.1099C>G","MODERATE","367/507",8,{"$nulls":5},"5","749","673","616","548","651","591","0","0","0","0.0558",{"$nulls":20},"0.691451","-0.76","1.035","1","0.06","0.001","0.304","0.148",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","746,0","0","746","0/1","626,37","0.0558","663",null,"chr9:133473538:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.062"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC41A3","chr3:126015510","SLC41A3(F318L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe318Leu","c.954T>G","MODERATE","318/507",8,{"$nulls":5},"5","469","535","354","386","392","450","0","0","0","0.1622",{"$nulls":20},"0.511454","1.55","2.53;.;.;2.53;.","0.851965;0.928021;0.851965;0.851965;0.851965","-5.14;-5.08;-5.14;-5.14;-5.08",".;0.142;0.047;0.172;.","0.069;0.041;0.047;0.039;0.055","0.372;0.363;0.367;0.362;0.365",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","455,0","0","455","0/1","430,80","0.1569","510",null,"chr3:126015510:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1554"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC41A3","chr3:126015510","SLC41A3(F318L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe318Leu","c.954T>G","MODERATE","318/507",8,{"$nulls":5},"5","469","319","354","240","390","277","0","0","0","0.4332",{"$nulls":20},"0.511454","1.55","2.53;.;.;2.53;.","0.851965;0.928021;0.851965;0.851965;0.851965","-5.14;-5.08;-5.14;-5.14;-5.08",".;0.142;0.047;0.172;.","0.069;0.041;0.047;0.039;0.055","0.372;0.363;0.367;0.362;0.365",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","455,0","0","455","0/1","169,137","0.4477","306",null,"chr3:126015510:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4625"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC4A1AP","chr2:27667273","SLC4A1AP(D343H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp343His","c.1027G>C","MODERATE","343/796",3,{"$nulls":5},"5","522","692","394","546","421","569","0","0","0","0.2074",{"$nulls":20},"4.214958","0.15;.;.;.","3.07;3.07;.;.","1","-5.71;.;.;.","1.0;1.0;.;.","0.001;.;.;.","0.684;0.686;0.672;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","503,0","0","503","0/1","540,125","0.188","665",null,"chr2:27667273:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1758"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC4A1AP","chr2:27667273","SLC4A1AP(D343H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp343His","c.1027G>C","MODERATE","343/796",3,{"$nulls":5},"5","522","451","394","343","420","367","0","0","0","0.3869",{"$nulls":20},"4.214958","0.15;.;.;.","3.07;3.07;.;.","1","-5.71;.;.;.","1.0;1.0;.;.","0.001;.;.;.","0.684;0.686;0.672;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","503,0","0","503","0/1","250,168","0.4019","418",null,"chr2:27667273:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3732"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC4A4","chr4:71547639","SLC4A4(E875fs)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 3. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) [MIM:604278]: An extremely rare autosomal recessive syndrome characterized by short stature, profound proximal renal tubular acidosis, mental retardation, bilateral glaucoma, cataracts and bandkeratopathy. pRTA is due to a failure of the proximal tubular cells to reabsorb filtered bicarbonate from the urine, leading to urinary bicarbonate wasting and subsequent acidemia. {ECO:0000269|PubMed:10545938, ECO:0000269|PubMed:15471865, ECO:0000269|PubMed:15713912, ECO:0000269|PubMed:15930088, ECO:0000269|PubMed:16636648, ECO:0000269|PubMed:17661077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Loss of interaction with and stimulation by CA4 is the cause of retinitis pigmentosa type 17 (RP17).; ","FUNCTION: Electrogenic sodium/bicarbonate cotransporter with a Na(+):HCO3(-) stoichiometry varying from 1:2 to 1:3. May regulate bicarbonate influx/efflux at the basolateral membrane of cells and regulate intracellular pH. {ECO:0000269|PubMed:10069984, ECO:0000269|PubMed:12907161, ECO:0000269|PubMed:16636648, ECO:0000269|PubMed:16769890, ECO:0000269|PubMed:17661077, ECO:0000269|PubMed:29500354, ECO:0000269|PubMed:9235899, ECO:0000269|PubMed:9651366}.; ",{"$nulls":4},"p.Glu875fs","c.2622-6_2622delTTTCAGG","HIGH","874/1094",20,{"$nulls":5},"4","729","986","554","694","671","916","0","0","0","0.1605",{"$nulls":5},"(SLC4A4|ENSG00000080493|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Renal tubular acidosis, proximal, with ocular abnormalities and/or migraine","Dental; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C1970309","0/0","740,0","0","740","0/1","794,169","0.1755","963",null,"chr4:71547639:TGGTTTCA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1628"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC4A4","chr4:71547639","SLC4A4(E875fs)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform 3. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Renal tubular acidosis, proximal, with ocular abnormalities and mental retardation (pRTA-OA) [MIM:604278]: An extremely rare autosomal recessive syndrome characterized by short stature, profound proximal renal tubular acidosis, mental retardation, bilateral glaucoma, cataracts and bandkeratopathy. pRTA is due to a failure of the proximal tubular cells to reabsorb filtered bicarbonate from the urine, leading to urinary bicarbonate wasting and subsequent acidemia. {ECO:0000269|PubMed:10545938, ECO:0000269|PubMed:15471865, ECO:0000269|PubMed:15713912, ECO:0000269|PubMed:15930088, ECO:0000269|PubMed:16636648, ECO:0000269|PubMed:17661077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Loss of interaction with and stimulation by CA4 is the cause of retinitis pigmentosa type 17 (RP17).; ","FUNCTION: Electrogenic sodium/bicarbonate cotransporter with a Na(+):HCO3(-) stoichiometry varying from 1:2 to 1:3. May regulate bicarbonate influx/efflux at the basolateral membrane of cells and regulate intracellular pH. {ECO:0000269|PubMed:10069984, ECO:0000269|PubMed:12907161, ECO:0000269|PubMed:16636648, ECO:0000269|PubMed:16769890, ECO:0000269|PubMed:17661077, ECO:0000269|PubMed:29500354, ECO:0000269|PubMed:9235899, ECO:0000269|PubMed:9651366}.; ",{"$nulls":4},"p.Glu875fs","c.2622-6_2622delTTTCAGG","HIGH","874/1094",20,{"$nulls":5},"5","729","484","554","355","670","468","0","0","0","0.3504",{"$nulls":5},"(SLC4A4|ENSG00000080493|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/AR","Renal tubular acidosis, proximal, with ocular abnormalities and/or migraine","Dental; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C1970309","0/0","740,0","0","740","0/1","308,160","0.3419","468",null,"chr4:71547639:TGGTTTCA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3352"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLC6A6","chr3:14484925","SLC6A6(G695E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Sodium-dependent taurine and beta-alanine transporter. Chloride ions are necessary for optimal uptake. {ECO:0000269|PubMed:8382624}.; ",{"$nulls":4},"p.Gly695Glu","c.2084G>A","MODERATE","695/721",15,{"$nulls":5},"5","855","803","652","570","663","669","0","0","0","0.2765",{"$nulls":20},"2.800088",null,"0.55;.","0.658278",null,"0.112;.",null,"0.202;0.223",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","834,0","0","834","0/1","561,195","0.2579","756",null,"chr3:14484925:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2509"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLC6A6","chr3:14484925","SLC6A6(G695E)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Sodium-dependent taurine and beta-alanine transporter. Chloride ions are necessary for optimal uptake. {ECO:0000269|PubMed:8382624}.; ",{"$nulls":4},"p.Gly695Glu","c.2084G>A","MODERATE","695/721",15,{"$nulls":5},"5","855","401","652","286","662","338","0","0","0","0.6923",{"$nulls":20},"2.800088",null,"0.55;.","0.658278",null,"0.112;.",null,"0.202;0.223",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","834,0","0","834","0/1","122,247","0.6694","369",null,"chr3:14484925:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6399"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLCO1C1","chr12:20737213","SLCO1C1(T497P)",null,null,"topological domain (Extracellular ), domain (Kazal-like ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs1464299256",-1,null,"FUNCTION: Mediates the Na(+)-independent high affinity transport of organic anions such as the thyroid hormones thyroxine (T4) and rT3. Other potential substrates, such as triiodothyronine (T3), 17-beta-glucuronosyl estradiol, estrone-3-sulfate and sulfobromophthalein (BSP) are transported with much lower efficiency. May play a signifiant role in regulating T4 flux into and out of the brain (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Thr497Pro","c.1489A>C","MODERATE","497/730",12,{"$nulls":5},"5","246","551","162","364","227","509","0","0","0","0.0943",{"$nulls":20},"4.004782","3.02",".;3.465;3.465;.","0.999999;1;0.999999;1;1","-5.2;-5.19;-5.38;-5.06",".;1.0;.;.","0.001;0.001;0.001;0.002","0.703;0.71;0.715;0.698",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","242,0","0","242","0/1","487,55","0.1015","542",null,"chr12:20737213:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1016"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLCO1C1","chr12:20737213","SLCO1C1(T497P)",null,null,"topological domain (Extracellular ), domain (Kazal-like ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs1464299256",-1,null,"FUNCTION: Mediates the Na(+)-independent high affinity transport of organic anions such as the thyroid hormones thyroxine (T4) and rT3. Other potential substrates, such as triiodothyronine (T3), 17-beta-glucuronosyl estradiol, estrone-3-sulfate and sulfobromophthalein (BSP) are transported with much lower efficiency. May play a signifiant role in regulating T4 flux into and out of the brain (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Thr497Pro","c.1489A>C","MODERATE","497/730",12,{"$nulls":5},"5","246","593","162","396","228","543","0","0","0","0.1215",{"$nulls":20},"4.004782","3.02",".;3.465;3.465;.","0.999999;1;0.999999;1;1","-5.2;-5.19;-5.38;-5.06",".;1.0;.;.","0.001;0.001;0.001;0.002","0.703;0.71;0.715;0.698",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","242,0","0","242","0/1","501,73","0.1272","574",null,"chr12:20737213:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1162"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SLFN13","chr17:35444897","SLFN13(E262Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Endoribonuclease that cleaves tRNAs and rRNAs (PubMed:29563550). Cleaves tRNAs 11 nucleotides from the 3'- terminus at the acceptor stem (PubMed:29563550). Does not act on tRNA(Sec) (PubMed:29563550). Able to restrict HIV-1 virus replication; ability to inhibit HIV-1 replication is dependent on endoribonuclease activity (PubMed:29563550). {ECO:0000269|PubMed:29563550}.; ",{"$nulls":4},"p.Glu262Gln","c.784G>C","MODERATE","262/897",3,{"$nulls":5},"5","548","513","444","427","460","440","0","0","0","0.3114",{"$nulls":20},"0.950261","0.28","3.345","1;1;1;1;0.999997;0.999997","-2.4;-2.4;-2.4;.","0.415","0.006;0.006;0.006;.","0.199;0.202;0.199;0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","543,0","0","543","0/1","348,156","0.3095","504",null,"chr17:35444897:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3115"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SLFN13","chr17:35444897","SLFN13(E262Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Endoribonuclease that cleaves tRNAs and rRNAs (PubMed:29563550). Cleaves tRNAs 11 nucleotides from the 3'- terminus at the acceptor stem (PubMed:29563550). Does not act on tRNA(Sec) (PubMed:29563550). Able to restrict HIV-1 virus replication; ability to inhibit HIV-1 replication is dependent on endoribonuclease activity (PubMed:29563550). {ECO:0000269|PubMed:29563550}.; ",{"$nulls":4},"p.Glu262Gln","c.784G>C","MODERATE","262/897",3,{"$nulls":5},"5","548","337","444","260","460","289","0","0","0","0.6644",{"$nulls":20},"0.950261","0.28","3.345","1;1;1;1;0.999997;0.999997","-2.4;-2.4;-2.4;.","0.415","0.006;0.006;0.006;.","0.199;0.202;0.199;0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","538,0","0","538","0/1","98,217","0.6889","315",null,"chr17:35444897:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6692"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SMC5","chr9:70280843","SMC5(E255Q)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). Required for recruitment of telomeres to PML nuclear bodies. Required for sister chromatid cohesion during prometaphase and mitotic progression; the function seems to be independent of SMC6. SMC5-SMC6 complex may prevent transcription of episomal DNA, such as circular viral DNA genome (PubMed:26983541). {ECO:0000269|PubMed:16810316, ECO:0000269|PubMed:17589526, ECO:0000269|PubMed:19502785, ECO:0000269|PubMed:26983541}.; ",{"$nulls":4},"p.Glu255Gln","c.763G>C","MODERATE","255/1101",6,{"$nulls":5},"5","201","259","144","169","166","211","0","0","0","0.1137",{"$nulls":20},"2.949531","-1.3","0.785","0.993526","-1.77","0.791","0.081","0.644",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","193,0","0","193","0/1","213,31","0.127","244",null,"chr9:70280843:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1183"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SMC5","chr9:70280843","SMC5(E255Q)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). Required for recruitment of telomeres to PML nuclear bodies. Required for sister chromatid cohesion during prometaphase and mitotic progression; the function seems to be independent of SMC6. SMC5-SMC6 complex may prevent transcription of episomal DNA, such as circular viral DNA genome (PubMed:26983541). {ECO:0000269|PubMed:16810316, ECO:0000269|PubMed:17589526, ECO:0000269|PubMed:19502785, ECO:0000269|PubMed:26983541}.; ",{"$nulls":4},"p.Glu255Gln","c.763G>C","MODERATE","255/1101",6,{"$nulls":5},"5","201","147","144","106","167","116","0","0","0","0.3276",{"$nulls":20},"2.949531","-1.3","0.785","0.993526","-1.77","0.791","0.081","0.644",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","193,0","0","193","0/1","93,43","0.3162","136",null,"chr9:70280843:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3208"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SMG1","chr16:18848011","SMG1(I1882M)",null,null,"region of interest (Interaction with SMG8 and SMG9 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine protein kinase involved in both mRNA surveillance and genotoxic stress response pathways. Recognizes the substrate consensus sequence [ST]-Q. Plays a central role in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by phosphorylating UPF1/RENT1. Recruited by release factors to stalled ribosomes together with SMG8 and SMG9 (forming the SMG1C protein kinase complex), and UPF1 to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Also acts as a genotoxic stress-activated protein kinase that displays some functional overlap with ATM. Can phosphorylate p53/TP53 and is required for optimal p53/TP53 activation after cellular exposure to genotoxic stress. Its depletion leads to spontaneous DNA damage and increased sensitivity to ionizing radiation (IR). May activate PRKCI but not PRKCZ. {ECO:0000269|PubMed:11331269, ECO:0000269|PubMed:11544179, ECO:0000269|PubMed:15175154, ECO:0000269|PubMed:16452507}.; ",{"$nulls":4},"p.Ile1882Met","c.5646T>G","MODERATE","1882/3661",37,{"$nulls":5},"4","158","122","111","86",null,null,"0","0",{"$nulls":22},"1.692631","5.3;5.23","0.115;.","0.74288","-0.68;.","0.718;.","0.159;.","0.477;.",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a protein involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their full-length nature has yet to be determined. [provided by RefSeq, Mar 2013].  ",null,null,"0/0","158,0","0","158","0/1","111,7","0.0593","118",null,"chr16:18848011:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0581"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SOX5","chr12:23665513","SOX5(R288W)",{"$nulls":6},255,"PASS","Missense","rs557463084",7.5642965204236008E-4,"DISEASE: Lamb-Shaffer syndrome (LAMSHF) [MIM:616803]: An autosomal dominant, neurodevelopmental disorder characterized by global developmental delay, intellectual disability, language and motor impairment, and distinct facial features. Additional variable skeletal abnormalities may also be present. {ECO:0000269|PubMed:22290657, ECO:0000269|PubMed:23220431, ECO:0000269|PubMed:23498568, ECO:0000269|PubMed:26111154}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Binds specifically to the DNA sequence 5'-AACAAT-3'. Activates transcription of COL2A1 and AGC1 in vitro.; ",{"$nulls":4},"p.Arg288Trp","c.862C>T","MODERATE","288/763",7,2,{"$nulls":4},"5","279","783","199","551","252","680","0","0","0","0.0603",{"$nulls":20},"4.550415","-4.48;-4.38;-4.49;-4.45;-4.38;.;-4.48",".;.;0.695;.;.;.;.","0.999999;0.999999;0.999996;0.999993;0.999999;0.999999;0.999993","-5.42;-5.32;-5.42;-5.42;-5.32;.;-5.42",".;1.0;1.0;1.0;1.0;1.0;.","0.0;0.0;0.0;0.0;0.0;.;0.0","0.865;0.901;0.882;0.896;0.904;.;0.903",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":6},"C4225202","0/0","274,0","0","274","0/1","707,47","0.0623","754",null,"chr12:23665513:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.069"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SPAG1","chr8:100165941","SPAG1(E90K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the cytoplasmic assembly of the ciliary dynein arms (By similarity). May play a role in fertilization. Binds GTP and has GTPase activity. {ECO:0000250, ECO:0000269|PubMed:11517287, ECO:0000269|PubMed:1299558}.; ",{"$nulls":4},"p.Glu90Lys","c.268G>A","MODERATE","90/926",3,{"$nulls":5},"5","130","173","88","121","117","162","0","0","0","0.0679",{"$nulls":20},"3.8731780000000002","2.25","2.78","0.999005;0.999005;0.999678;0.999678","-3.07;-2.55;-3.07;-2.55",".;0.908;.;0.908","0.122;0.032;0.122;0.032","0.326;0.233;0.324;0.236",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The correlation of anti-sperm antibodies with cases of unexplained infertility implicates a role for these antibodies in blocking fertilization. Improved diagnosis and treatment of immunologic infertility, as well as identification of proteins for targeted contraception, are dependent on the identification and characterization of relevant sperm antigens. The protein expressed by this gene is recognized by anti-sperm agglutinating antibodies from an infertile woman. Furthermore, immunization of female rats with the recombinant human protein reduced fertility. This protein localizes to the plasma membrane of germ cells in the testis and to the post-acrosomal plasma membrane of mature spermatozoa. Recombinant polypeptide binds GTP and exhibits GTPase activity. Thus, this protein may regulate GTP signal transduction pathways involved in spermatogenesis and fertilization. Two transcript variants of this gene encode the same protein. [provided by RefSeq, Jul 2008].",null,"C3809706","0/0","124,0","0","124","0/1","157,11","0.0655","168",null,"chr8:100165941:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0661"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SPAG8","chr9:35811525","SPAG8(G174D)",{"$nulls":6},255,"PASS","Missense","rs746851192",1.619e-05,null,"FUNCTION: Plays a role in spermatogenesis by enhancing the binding of CREM isoform tau to its coactivator FHL5 and increasing the FHL5-regulated transcriptional activation of CREM isoform tau (By similarity). Involved in the acrosome reaction and in binding of sperm to the zona pellucida (By similarity). Plays a role in regulation of the cell cycle by controlling progression through the G2/M phase, possibly by delaying the activation of CDK1 which is required for entry into mitosis (PubMed:19548270). May play a role in fertility and microtubule formation through interaction with RANBP9 (PubMed:10500252). {ECO:0000250|UniProtKB:Q3V0Q6, ECO:0000269|PubMed:10500252, ECO:0000269|PubMed:19548270}.; ",{"$nulls":4},"p.Gly174Asp","c.521G>A","MODERATE","174/501",2,{"$nulls":5},"5","319","170","250","137","249","119","0","0","0","0.2437",{"$nulls":20},"1.280282","-2.12","1.04;.;1.04","1","-2.36;-1.93;-2.09","0.98;.;.","0.024","0.17;0.139;0.131",{"$nulls":3},"ExAC_NFE_AF",1.619e-05,{"$nulls":7},"0/0","318,1","0.0031","319","0/1","117,52","0.3077","169",null,"chr9:35811525:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3066"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SPHKAP","chr2:228132071","SPHKAP(S16*)",{"$nulls":6},255,"PASS","Loss Of Function","rs756302311",1.5020000000000002E-5,null,"FUNCTION: Anchoring protein that binds preferentially to the type I regulatory subunit of c-AMP-dependent protein kinase (PKA type I) and targets it to distinct subcellular compartments. May act as a converging factor linking cAMP and sphingosine signaling pathways. Plays a regulatory role in the modulation of SPHK1. {ECO:0000269|PubMed:12080051, ECO:0000269|PubMed:20394097}.; ",{"$nulls":4},"p.Ser16*","c.47C>G","HIGH","16/1700",2,{"$nulls":5},"4","318","405","200","261","294","375","0","0","0","0.216",{"$nulls":5},"(SPHKAP|ENSG00000153820|1|1.00)","(SPHKAP|ENSG00000153820|1|1.00)",{"$nulls":13},"7.703508",null,null,"1",{"$nulls":3},"0.348;0.349",{"$nulls":3},"ExAC_NFE_AF",1.5020000000000002E-5,{"$nulls":7},"0/0","316,0","0","316","0/1","301,97","0.2437","398",null,"chr2:228132071:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2299"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SPHKAP","chr2:228132071","SPHKAP(S16*)",{"$nulls":6},255,"PASS","Loss Of Function","rs756302311",1.5020000000000002E-5,null,"FUNCTION: Anchoring protein that binds preferentially to the type I regulatory subunit of c-AMP-dependent protein kinase (PKA type I) and targets it to distinct subcellular compartments. May act as a converging factor linking cAMP and sphingosine signaling pathways. Plays a regulatory role in the modulation of SPHK1. {ECO:0000269|PubMed:12080051, ECO:0000269|PubMed:20394097}.; ",{"$nulls":4},"p.Ser16*","c.47C>G","HIGH","16/1700",2,{"$nulls":5},"4","318","173","200","120","296","156","0","0","0","0.3269",{"$nulls":5},"(SPHKAP|ENSG00000153820|1|1.00)","(SPHKAP|ENSG00000153820|1|1.00)",{"$nulls":13},"7.703508",null,null,"1",{"$nulls":3},"0.348;0.349",{"$nulls":3},"ExAC_NFE_AF",1.5020000000000002E-5,{"$nulls":7},"0/0","316,0","0","316","0/1","111,59","0.3471","170",null,"chr2:228132071:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.35"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SPINT1","chr15:40853879","SPINT1(Q304R)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Inhibitor of HGF activator. Also acts as an inhibitor of matriptase (ST14).; ",{"$nulls":5},"c.911A>G","HIGH",null,5,{"$nulls":5},"5","304","457","227","340","268","398","0","0","0","0.1106",{"$nulls":20},"2.161977","-3.65;-3.7;-3.67;-4.35","0;0;.;.","1;0.886042;0.999499;0.995811;0.886042","-0.53;-0.24;-0.56;-0.73","0.019;0.008;.;.","0.49;0.557;0.191;0.239","0.094;0.058;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","303,0","0","303","0/1","395,51","0.1143","446",null,"chr15:40853879:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1088"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SPINT1","chr15:40853879","SPINT1(Q304R)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Inhibitor of HGF activator. Also acts as an inhibitor of matriptase (ST14).; ",{"$nulls":5},"c.911A>G","HIGH",null,5,{"$nulls":5},"5","304","393","227","304","269","345","0","0","0","0.1594",{"$nulls":20},"2.161977","-3.65;-3.7;-3.67;-4.35","0;0;.;.","1;0.886042;0.999499;0.995811;0.886042","-0.53;-0.24;-0.56;-0.73","0.019;0.008;.;.","0.49;0.557;0.191;0.239","0.094;0.058;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","303,0","0","303","0/1","324,63","0.1628","387",null,"chr15:40853879:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1579"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SSPO","chr7:149792335","SSPO(E1860A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the modulation of neuronal aggregation. May be involved in developmental events during the formation of the central nervous system (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu1860Ala","c.5579A>C","MODERATE","1860/5150",36,{"$nulls":5},"5","205","160","183","144","170","133","0","0","0","0.3308",{"$nulls":20},"1.148713",{"$nulls":6},"0.319",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","201,0","0","201","0/1","112,49","0.3043","161",null,"chr7:149792335:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3125"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SSPO","chr7:149792335","SSPO(E1860A)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the modulation of neuronal aggregation. May be involved in developmental events during the formation of the central nervous system (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu1860Ala","c.5579A>C","MODERATE","1860/5150",36,{"$nulls":5},"5","205","111","183","102","170","95","0","0","0","0.7368",{"$nulls":20},"1.148713",{"$nulls":6},"0.319",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","199,0","0","199","0/1","37,76","0.6726","113",null,"chr7:149792335:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6569"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","STIP1","chr11:64195787","STIP1(E263Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a co-chaperone for HSP90AA1 (PubMed:27353360). Mediates the association of the molecular chaperones HSPA8/HSC70 and HSP90 (By similarity). {ECO:0000250|UniProtKB:O35814, ECO:0000303|PubMed:27353360}.; ",{"$nulls":4},"p.Glu263Gln","c.787G>C","MODERATE","263/590",5,1,{"$nulls":4},"5","98","74","74","51","86","62","0","0","0","0.0645",{"$nulls":20},"3.509455","2.3;2.57;2.3;-0.82",".;2.93;.;.","1","-1.65;-1.64;-1.67;-1.75",".;0.991;.;0.999","0.083;0.062;0.057;0.01","0.226;0.242;0.274;0.232",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","97,0","0","97","0/1","61,6","0.0896","67",null,"chr11:64195787:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0784"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","STRA6","chr15:74191228","STRA6(K307N)",null,null,"transmembrane region (Helical ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Microphthalmia, syndromic, 9 (MCOPS9) [MIM:601186]: A rare clinical entity including as main characteristics anophthalmia or severe microphthalmia, and pulmonary hypoplasia or aplasia. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269|PubMed:17273977, ECO:0000269|PubMed:17503335, ECO:0000269|PubMed:21368206, ECO:0000269|PubMed:21901792}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Mutations in STRA6 may be a cause of isolated colobomatous microphthalmia, a disorder of the eye characterized by an abnormally small ocular globe. {ECO:0000269|PubMed:21901792}.; ","FUNCTION: Functions as retinol transporter. Accepts all-trans retinol from the extracellular retinol-binding protein RBP4, facilitates retinol transport across the cell membrane, and then transfers retinol to the cytoplasmic retinol-binding protein RBP1 (PubMed:9452451, PubMed:18316031, PubMed:22665496). Retinol uptake is enhanced by LRAT, an enzyme that converts retinol to all-trans retinyl esters, the storage forms of vitamin A (PubMed:18316031, PubMed:22665496). Contributes to the activation of a signaling cascade that depends on retinol transport and LRAT-dependent generation of retinol metabolites that then trigger activation of JAK2 and its target STAT5, and ultimately increase the expression of SOCS3 and inhibit cellular responses to insulin (PubMed:21368206, PubMed:22665496). Important for the homeostasis of vitamin A and its derivatives, such as retinoic acid (PubMed:18316031). STRA6-mediated transport is particularly important in the eye, and under conditions of dietary vitamin A deficiency (Probable). Does not transport retinoic acid (PubMed:18316031). {ECO:0000269|PubMed:18316031, ECO:0000269|PubMed:21901792, ECO:0000269|PubMed:22665496, ECO:0000269|PubMed:9452451, ECO:0000305}.; ",{"$nulls":4},"p.Lys307Asn","c.921G>C","MODERATE","307/706",10,{"$nulls":5},"5","476","342","353","243","444","308","0","0","0","0.1786",{"$nulls":20},"2.516384","-1.52;-1.52;-1.52;-1.52;-1.52;.;-1.52;-1.52;-1.52","2.015;.;2.015;2.015;.;2.015;.;.;.","0.720099;0.720099;0.720099;0.720099;0.720099;0.593688;0.593688;0.720099","-1.46;-1.56;-1.46;.;.;.;-1.46;.;.","0.012;0.012;0.012;0.012;.;0.012;.;0.029;.","0.041;0.042;0.041;.;.;.;0.033;.;.","0.234;0.215;0.234;0.234;0.245;0.234;0.246;0.239;0.246",{"$nulls":3},"Unknown",-1,"AR","Microphthalmia, syndromic 9; Microphthalmia, isolated, with coloboma 8","Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Pulmonary; Renal",{"$nulls":3},"C1832661","0/0","468,0","0","468","0/1","272,63","0.1881","335",null,"chr15:74191228:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2016"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SUGCT","chr7:40135055","SUGCT(R19L)",null,null,"transit peptide (Mitochondrion )",{"$nulls":3},255,"PASS","Missense","rs752451426",1.517E-4,null,"FUNCTION: Catalyzes the succinyl-CoA-dependent conversion of glutarate to glutaryl-CoA. Can use different dicarboxylic acids as CoA acceptors, the preferred ones are glutarate, succinate, adipate, and 3-hydroxymethylglutarate. {ECO:0000269|PubMed:23893049}.; ",{"$nulls":4},"p.Arg19Leu","c.56G>T","MODERATE","19/471",1,{"$nulls":5},"5","410","386","331","321","340","337","0","0","0","0.1454",{"$nulls":20},"2.597218","0.87;.;0.89","1.04","0.999997","-1.66;.;-1.56",null,"0.296;.;0.41","0.367;0.35;0.342",{"$nulls":3},"ExAC_NFE_AF",1.517E-4,"AR","Glutaric aciduria III","Biochemical",{"$nulls":3},"C0342873","0/0","402,0","0","402","0/1","321,57","0.1508","378",null,"chr7:40135055:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.134"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SUN1","chr7:852018","SUN1(W313R)",null,null,"topological domain (Nuclear ), splice variant (In isoform 4. ), splice variant (In isoform 3. ), splice variant (In isoform 2 and isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton (PubMed:18039933, PubMed:18396275). The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning (By similarity). Required for interkinetic nuclear migration (INM) and essential for nucleokinesis and centrosome-nucleus coupling during radial neuronal migration in the cerebral cortex and during glial migration (By similarity). Involved in telomere attachment to nuclear envelope in the prophase of meiosis implicating a SUN1/2:KASH5 LINC complex in which SUN1 and SUN2 seem to act at least partial redundantly (By similarity). Required for gametogenesis and involved in selective gene expression of coding and non-coding RNAs needed for gametogenesis (By similarity). Helps to define the distribution of nuclear pore complexes (NPCs) (By similarity). Required for efficient localization of SYNE4 in the nuclear envelope (By similarity). May be involved in nuclear remodeling during sperm head formation in spermatogenenis (By similarity). May play a role in DNA repair by suppressing non- homologous end joining repair to facilitate the repair of DNA cross-links (PubMed:24375709). {ECO:0000250|UniProtKB:Q9D666, ECO:0000269|PubMed:18039933, ECO:0000269|PubMed:18396275, ECO:0000269|PubMed:24375709}.; ",{"$nulls":4},"p.Trp313Arg","c.937T>A","MODERATE","313/822",8,{"$nulls":5},"4","732","1029","489","671","686","948","0.0014","0.0014","0","0.2384",{"$nulls":20},"4.356974","0.92",null,"0.728784;0.728784;0.77772;0.728784;0.52838;0.777948;0.537511","-7.87;-7.44;-7.02;-7.48;-7.87;-7.2;-7.01","0.999;.;.;.;0.999;.;.","0.003;0.018;0.004;0.004;0.003;0.023;0.004","0.689;0.72;0.746;0.697;0.688;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","715,1","0.0014","716","0/1","742,243","0.2467","985",null,"chr7:852018:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2399"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SUN1","chr7:852018","SUN1(W313R)",null,null,"topological domain (Nuclear ), splice variant (In isoform 4. ), splice variant (In isoform 3. ), splice variant (In isoform 2 and isoform 7. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton (PubMed:18039933, PubMed:18396275). The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning (By similarity). Required for interkinetic nuclear migration (INM) and essential for nucleokinesis and centrosome-nucleus coupling during radial neuronal migration in the cerebral cortex and during glial migration (By similarity). Involved in telomere attachment to nuclear envelope in the prophase of meiosis implicating a SUN1/2:KASH5 LINC complex in which SUN1 and SUN2 seem to act at least partial redundantly (By similarity). Required for gametogenesis and involved in selective gene expression of coding and non-coding RNAs needed for gametogenesis (By similarity). Helps to define the distribution of nuclear pore complexes (NPCs) (By similarity). Required for efficient localization of SYNE4 in the nuclear envelope (By similarity). May be involved in nuclear remodeling during sperm head formation in spermatogenenis (By similarity). May play a role in DNA repair by suppressing non- homologous end joining repair to facilitate the repair of DNA cross-links (PubMed:24375709). {ECO:0000250|UniProtKB:Q9D666, ECO:0000269|PubMed:18039933, ECO:0000269|PubMed:18396275, ECO:0000269|PubMed:24375709}.; ",{"$nulls":4},"p.Trp313Arg","c.937T>A","MODERATE","313/822",8,{"$nulls":5},"4","732","605","489","405","687","539","0.0014","0.0014","0","0.2245",{"$nulls":20},"4.356974","0.92",null,"0.728784;0.728784;0.77772;0.728784;0.52838;0.777948;0.537511","-7.87;-7.44;-7.02;-7.48;-7.87;-7.2;-7.01","0.999;.;.;.;0.999;.;.","0.003;0.018;0.004;0.004;0.003;0.023;0.004","0.689;0.72;0.746;0.697;0.688;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","717,1","0.0014","718","0/1","426,153","0.2642","579",null,"chr7:852018:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2346"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SYBU","chr8:109575907","SYBU(R336fs)",null,null,"region of interest (Sufficient for interaction with KIF5B ), region of interest (Sufficient for interaction with STX1A ), coiled-coil region ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Part of a kinesin motor-adapter complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. {ECO:0000250, ECO:0000269|PubMed:15459722}.; ",{"$nulls":4},"p.Arg336fs","c.1005dupC","HIGH","335/668",9,{"$nulls":5},"5","390","455","284","316","340","386","0","0","0","0.0959",{"$nulls":5},"(SYBU|ENSG00000147642|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development (Cai et al., 2007 [PubMed 17611281]).[supplied by OMIM, Mar 2008].",null,null,"0/0","360,0","0","360","0/1","363,42","0.1037","405",null,"chr8:109575907:T:TG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1013"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SYBU","chr8:109575907","SYBU(R336fs)",null,null,"region of interest (Sufficient for interaction with KIF5B ), region of interest (Sufficient for interaction with STX1A ), coiled-coil region ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Part of a kinesin motor-adapter complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development. {ECO:0000250, ECO:0000269|PubMed:15459722}.; ",{"$nulls":4},"p.Arg336fs","c.1005dupC","HIGH","335/668",9,{"$nulls":5},"5","390","337","284","245","338","283","0","0","0","0.1979",{"$nulls":5},"(SYBU|ENSG00000147642|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development (Cai et al., 2007 [PubMed 17611281]).[supplied by OMIM, Mar 2008].",null,null,"0/0","360,0","0","360","0/1","231,61","0.2089","292",null,"chr8:109575907:T:TG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1673"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","SYN1","chrX:47575229","SYN1(D402H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Epilepsy X-linked, with variable learning disabilities and behavior disorders (XELBD) [MIM:300491]: A neurologic disorder characterized by variable combinations of epilepsy, learning difficulties, macrocephaly, and aggressive behavior. {ECO:0000269|PubMed:14985377}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. The complex formed with NOS1 and CAPON proteins is necessary for specific nitric-oxid functions at a presynaptic level.; ","epilepsy",{"$nulls":3},"p.Asp402His","c.1204G>C","MODERATE","402/705",10,{"$nulls":5},"4","1127","1207","853","864","934","1050","0","0","0","0.2781",{"$nulls":20},"4.029806","0.31;-0.26","3.16","1","-6.2","1.0","0.0","0.884;0.883",{"$nulls":3},"Unknown",-1,"XL","Epilepsy, X-linked, with variable learning disabilities and behavior disorders","Neurologic",null,"This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein encoded serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations in this gene may be associated with X-linked disorders with primary neuronal degeneration such as Rett syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008].",null,"C1845343","0/0","1093,0","0","1093","0/1","830,317","0.2764","1147",null,"chrX:47575229:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.265"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","SYN1","chrX:47575229","SYN1(D402H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Epilepsy X-linked, with variable learning disabilities and behavior disorders (XELBD) [MIM:300491]: A neurologic disorder characterized by variable combinations of epilepsy, learning difficulties, macrocephaly, and aggressive behavior. {ECO:0000269|PubMed:14985377}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. The complex formed with NOS1 and CAPON proteins is necessary for specific nitric-oxid functions at a presynaptic level.; ","epilepsy",{"$nulls":3},"p.Asp402His","c.1204G>C","MODERATE","402/705",10,{"$nulls":5},"5","1127","989","853","710","934","836","0","0","0","0.4163",{"$nulls":20},"4.029806","0.31;-0.26","3.16","1","-6.2","1.0","0.0","0.884;0.883",{"$nulls":3},"Unknown",-1,"XL","Epilepsy, X-linked, with variable learning disabilities and behavior disorders","Neurologic",null,"This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein encoded serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations in this gene may be associated with X-linked disorders with primary neuronal degeneration such as Rett syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008].",null,"C1845343","0/0","1094,0","0","1094","0/1","538,389","0.4196","927",null,"chrX:47575229:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4085"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TAT","chr16:71572192","TAT(L234V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Tyrosinemia 2 (TYRSN2) [MIM:276600]: An inborn error of metabolism characterized by elevations of tyrosine in the blood and urine, and oculocutaneous manifestations. Typical features include palmoplantar keratosis, painful corneal ulcers, and mental retardation. {ECO:0000269|PubMed:1357662}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transaminase involved in tyrosine breakdown. Converts tyrosine to p-hydroxyphenylpyruvate. Can catalyze the reverse reaction, using glutamic acid, with 2-oxoglutarate as cosubstrate (in vitro). Has much lower affinity and transaminase activity towards phenylalanine. {ECO:0000269|PubMed:16640556, ECO:0000269|PubMed:7999802}.; ",{"$nulls":4},"p.Leu234Val","c.700C>G","MODERATE","234/454",6,{"$nulls":5},"5","166","166","143","141","134","116","0","0","0","0.2241",{"$nulls":20},"2.109347","-2.8","1.615","1","-1.64","0.617","0.072","0.429",{"$nulls":3},"Unknown",-1,"AR","Tyrosinemia, type II","Biochemical; Dermatologic; Neurologic; Ophthalmologic",{"$nulls":3},"C0268487","0/0","163,0","0","163","0/1","130,34","0.2073","164",null,"chr16:71572192:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2128"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TAT","chr16:71572192","TAT(L234V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Tyrosinemia 2 (TYRSN2) [MIM:276600]: An inborn error of metabolism characterized by elevations of tyrosine in the blood and urine, and oculocutaneous manifestations. Typical features include palmoplantar keratosis, painful corneal ulcers, and mental retardation. {ECO:0000269|PubMed:1357662}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Transaminase involved in tyrosine breakdown. Converts tyrosine to p-hydroxyphenylpyruvate. Can catalyze the reverse reaction, using glutamic acid, with 2-oxoglutarate as cosubstrate (in vitro). Has much lower affinity and transaminase activity towards phenylalanine. {ECO:0000269|PubMed:16640556, ECO:0000269|PubMed:7999802}.; ",{"$nulls":4},"p.Leu234Val","c.700C>G","MODERATE","234/454",6,{"$nulls":5},"5","166","103","143","87","134","87","0","0","0","0.4713",{"$nulls":20},"2.109347","-2.8","1.615","1","-1.64","0.617","0.072","0.429",{"$nulls":3},"Unknown",-1,"AR","Tyrosinemia, type II","Biochemical; Dermatologic; Neurologic; Ophthalmologic",{"$nulls":3},"C0268487","0/0","163,0","0","163","0/1","56,46","0.451","102",null,"chr16:71572192:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4713"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","THBS2","chr6:169222310","THBS2(P1054S)",null,null,"domain (TSP C-terminal ), disulfide bond , strand ",{"$nulls":3},255,"PASS","Missense","rs1289777741",-1,null,"FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Ligand for CD36 mediating antiangiogenic properties. {ECO:0000269|PubMed:20714802}.; ","level2",{"$nulls":3},"p.Pro1054Ser","c.3160C>T","MODERATE","1054/1172",20,{"$nulls":5},"4","478","677","403","519",null,null,"0.0021","0.0021",{"$nulls":22},"3.973251","-4.23;.;.","2.34;.;2.34","1","-7.03;.;.","0.92;.;0.92","0.001;.;.","0.916;.;0.908",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kTGF_BETA",null,null,"C0158252","0/0","473,1","0.0021","474","0/1","424,222","0.3437","646",null,"chr6:169222310:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.343"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","THBS2","chr6:169222310","THBS2(P1054S)",null,null,"domain (TSP C-terminal ), disulfide bond , strand ",{"$nulls":3},255,"PASS","Missense","rs1289777741",-1,null,"FUNCTION: Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Ligand for CD36 mediating antiangiogenic properties. {ECO:0000269|PubMed:20714802}.; ","level2",{"$nulls":3},"p.Pro1054Ser","c.3160C>T","MODERATE","1054/1172",20,{"$nulls":5},"4","478","367","403","295",null,null,"0.0021","0.0021",{"$nulls":22},"3.973251","-4.23;.;.","2.34;.;2.34","1","-7.03;.;.","0.92;.;0.92","0.001;.;.","0.916;.;0.908",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kTGF_BETA",null,null,"C0158252","0/0","474,1","0.0021","475","0/1","212,150","0.4144","362",null,"chr6:169222310:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TNRC18","chr7:5371311","TNRC18(Y1095N)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Tyr1095Asn","c.3283T>A","MODERATE","1095/2968",11,{"$nulls":5},"5","369","448","302","351","305","371","0","0","0","0.1132",{"$nulls":20},"3.83362","2.61",".;1.935","0.719522","-4.41",".;0.999","0.003","0.7;0.683",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","365,0","0","365","0/1","393,42","0.0966","435",null,"chr7:5371311:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0969"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TOR1AIP2","chr1:179846555","TOR1AIP2(C310S)",null,null,"topological domain (Lumenal ), region of interest (Interaction with TOR1A ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for endoplasmic reticulum integrity. Regulates the distribution of TOR1A between the endoplasmic reticulum and the nuclear envelope as well as induces TOR1A, TOR1B and TOR3A ATPase activity. {ECO:0000269|PubMed:19339278, ECO:0000269|PubMed:23569223, ECO:0000269|PubMed:24275647}.; ",{"$nulls":4},"p.Cys310Ser","c.929G>C","MODERATE","310/470",6,{"$nulls":5},"4","607","717","447","508","545","653","0","0","0","0.1363",{"$nulls":20},"3.861359","1.14;.","2.25","1","-9.99;.","0.999","0.002;.","0.894;0.897",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","591,0","0","591","0/1","608,94","0.1339","702",null,"chr1:179846555:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1319"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TOR1AIP2","chr1:179846555","TOR1AIP2(C310S)",null,null,"topological domain (Lumenal ), region of interest (Interaction with TOR1A ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for endoplasmic reticulum integrity. Regulates the distribution of TOR1A between the endoplasmic reticulum and the nuclear envelope as well as induces TOR1A, TOR1B and TOR3A ATPase activity. {ECO:0000269|PubMed:19339278, ECO:0000269|PubMed:23569223, ECO:0000269|PubMed:24275647}.; ",{"$nulls":4},"p.Cys310Ser","c.929G>C","MODERATE","310/470",6,{"$nulls":5},"4","607","456","447","342","546","397","0","0","0","0.2343",{"$nulls":20},"3.861359","1.14;.","2.25","1","-9.99;.","0.999","0.002;.","0.894;0.897",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","593,0","0","593","0/1","338,110","0.2455","448",null,"chr1:179846555:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2485"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TP53","chr17:7674252","TP53(M198I)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In a sporadic cancer; somatic mutation. TP53(E198D)), sequence variant (In sporadic cancers; somatic mutation. TP53(E198G)), sequence variant (In sporadic cancers; somatic mutation. TP53(E198K)), sequence variant (In sporadic cancers; somatic mutation. TP53(E198Q)), sequence variant (In a sporadic cancer; somatic mutation. TP53(E198V)), strand ",{"$nulls":3},255,"PASS","Missense","rs587782664",6.0570000000000005E-5,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Met198Ile","c.594G>A","MODERATE","198/410",7,137,{"$nulls":4},"5","657","607","488","409","532","505","0","0","0","0.3287",{"$nulls":20},"3.903464","-6.77;-6.77;.;.;.;.;.;.;.;-6.77;.;.;-6.77;-6.77;.;.;-6.77;.;.;-6.77;-6.77",".;.;.;.;.;.;.;.;.;3.27;.;3.27;3.27;3.27;.;.;3.27;.;.;.;.","0.999983","-3.78;-3.89;.;.;.;.;.;.;.;-3.89;.;.;-3.89;-3.89;.;.;-3.89;.;.;-3.77;-3.54","1.0;.;.;.;.;.;.;.;.;1.0;.;1.0;0.975;1.0;.;.;1.0;.;.;.;0.999","0.008;0.007;.;.;.;.;.;.;.;0.007;.;.;0.006;0.007;.;.;0.007;.;.;0.008;0.009","0.9;0.919;0.858;0.877;0.867;0.847;0.881;0.86;0.91;0.937;0.91;0.917;0.921;0.917;0.877;0.82;0.937;0.91;0.886;.;.",{"$nulls":3},"ExAC_SAS_AF",6.0570000000000005E-5,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","640,0","0","640","0/1","381,195","0.3385","576",null,"chr17:7674252:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3325"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TP53","chr17:7674252","TP53(M198I)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In a sporadic cancer; somatic mutation. TP53(E198D)), sequence variant (In sporadic cancers; somatic mutation. TP53(E198G)), sequence variant (In sporadic cancers; somatic mutation. TP53(E198K)), sequence variant (In sporadic cancers; somatic mutation. TP53(E198Q)), sequence variant (In a sporadic cancer; somatic mutation. TP53(E198V)), strand ",{"$nulls":3},255,"PASS","Missense","rs587782664",6.0570000000000005E-5,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Met198Ile","c.594G>A","MODERATE","198/410",7,137,{"$nulls":4},"5","657","301","488","213","529","235","0","0","0","0.6851",{"$nulls":20},"3.903464","-6.77;-6.77;.;.;.;.;.;.;.;-6.77;.;.;-6.77;-6.77;.;.;-6.77;.;.;-6.77;-6.77",".;.;.;.;.;.;.;.;.;3.27;.;3.27;3.27;3.27;.;.;3.27;.;.;.;.","0.999983","-3.78;-3.89;.;.;.;.;.;.;.;-3.89;.;.;-3.89;-3.89;.;.;-3.89;.;.;-3.77;-3.54","1.0;.;.;.;.;.;.;.;.;1.0;.;1.0;0.975;1.0;.;.;1.0;.;.;.;0.999","0.008;0.007;.;.;.;.;.;.;.;0.007;.;.;0.006;0.007;.;.;0.007;.;.;0.008;0.009","0.9;0.919;0.858;0.877;0.867;0.847;0.881;0.86;0.91;0.937;0.91;0.917;0.921;0.917;0.877;0.82;0.937;0.91;0.886;.;.",{"$nulls":3},"ExAC_SAS_AF",6.0570000000000005E-5,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","651,0","0","651","0/1","87,206","0.7031","293",null,"chr17:7674252:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6854"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TRPM7","chr15:50643443","TRPM7(Q144H)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Amyotrophic lateral sclerosis-parkinsonism/dementia complex 1 (ALS-PDC1) [MIM:105500]: A neurodegenerative disorder characterized by chronic, progressive and uniformly fatal amyotrophic lateral sclerosis and parkinsonism-dementia. Both diseases are known to occur in the same kindred, the same sibship and even the same individual. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Essential ion channel and serine/threonine-protein kinase. Divalent cation channel permeable to calcium and magnesium. Has a central role in magnesium ion homeostasis and in the regulation of anoxic neuronal cell death. Involved in TNF- induced necroptosis downstream of MLKL by mediating calcium influx. The kinase activity is essential for the channel function. May be involved in a fundamental process that adjusts plasma membrane divalent cation fluxes according to the metabolic state of the cell. Phosphorylates annexin A1 (ANXA1). {ECO:0000269|PubMed:12887921, ECO:0000269|PubMed:15485879, ECO:0000269|PubMed:24316671}.; ",{"$nulls":4},"p.Gln144His","c.432G>T","MODERATE","144/1865",5,{"$nulls":5},"5","482","661","373","468","394","555","0","0","0","0.1261",{"$nulls":20},"3.252434",".;4.06;4.06","2.44;2.44;.","0.999947",".;-4.09;-4.09","0.834;0.834;.",".;0.033;0.034",".;0.556;0.587",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0543859","0/0","460,0","0","460","0/1","534,83","0.1345","617",null,"chr15:50643443:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1197"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TRPM7","chr15:50643443","TRPM7(Q144H)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Amyotrophic lateral sclerosis-parkinsonism/dementia complex 1 (ALS-PDC1) [MIM:105500]: A neurodegenerative disorder characterized by chronic, progressive and uniformly fatal amyotrophic lateral sclerosis and parkinsonism-dementia. Both diseases are known to occur in the same kindred, the same sibship and even the same individual. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Essential ion channel and serine/threonine-protein kinase. Divalent cation channel permeable to calcium and magnesium. Has a central role in magnesium ion homeostasis and in the regulation of anoxic neuronal cell death. Involved in TNF- induced necroptosis downstream of MLKL by mediating calcium influx. The kinase activity is essential for the channel function. May be involved in a fundamental process that adjusts plasma membrane divalent cation fluxes according to the metabolic state of the cell. Phosphorylates annexin A1 (ANXA1). {ECO:0000269|PubMed:12887921, ECO:0000269|PubMed:15485879, ECO:0000269|PubMed:24316671}.; ",{"$nulls":4},"p.Gln144His","c.432G>T","MODERATE","144/1865",5,{"$nulls":5},"5","482","381","373","282","393","318","0","0","0","0.239",{"$nulls":20},"3.252434",".;4.06;4.06","2.44;2.44;.","0.999947",".;-4.09;-4.09","0.834;0.834;.",".;0.033;0.034",".;0.556;0.587",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C0543859","0/0","461,0","0","461","0/1","283,75","0.2095","358",null,"chr15:50643443:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2234"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TSC2","chr16:2081786","TSC2(R1268G)",null,null,"splice variant (In isoform 8. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Tuberous sclerosis 2 (TSC2) [MIM:613254]: An autosomal dominant multi-system disorder that affects especially the brain, kidneys, heart, and skin. It is characterized by hamartomas (benign overgrowths predominantly of a cell or tissue type that occurs normally in the organ) and hamartias (developmental abnormalities of tissue combination). Clinical manifestations include epilepsy, learning difficulties, behavioral problems, and skin lesions. Seizures can be intractable and premature death can occur from a variety of disease-associated causes. {ECO:0000269|PubMed:10069705, ECO:0000269|PubMed:10205261, ECO:0000269|PubMed:10533067, ECO:0000269|PubMed:10570911, ECO:0000269|PubMed:10607950, ECO:0000269|PubMed:10732801, ECO:0000269|PubMed:10735580, ECO:0000269|PubMed:12271141, ECO:0000269|PubMed:15024740, ECO:0000269|PubMed:15340059, ECO:0000269|PubMed:15595939, ECO:0000269|PubMed:15963462, ECO:0000269|PubMed:8824881, ECO:0000269|PubMed:9302281, ECO:0000269|PubMed:9463313, ECO:0000269|PubMed:9829910}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Lymphangioleiomyomatosis (LAM) [MIM:606690]: Progressive and often fatal lung disease characterized by a diffuse proliferation of abnormal smooth muscle cells in the lungs. It affects almost exclusively young women and can occur as an isolated disorder or in association with tuberous sclerosis complex. {ECO:0000269|PubMed:10823953, ECO:0000269|PubMed:11829138}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Focal cortical dysplasia 2 (FCORD2) [MIM:607341]: A form of focal cortical dysplasia, a malformation of cortical development that results in medically refractory epilepsy in the pediatric population and in adults. FCORD2 is a severe form, with onset usually in childhood, characterized by disrupted cortical lamination and specific cytological abnormalities. It is classified in 2 subtypes: type IIA characterized by dysmorphic neurons and lack of balloon cells; type IIB with dysmorphic neurons and balloon cells. {ECO:0000269|PubMed:28215400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: In complex with TSC1, this tumor suppressor inhibits the nutrient-mediated or growth factor-stimulated phosphorylation of S6K1 and EIF4EBP1 by negatively regulating mTORC1 signaling (PubMed:12271141, PubMed:28215400). Acts as a GTPase-activating protein (GAP) for the small GTPase RHEB, a direct activator of the protein kinase activity of mTORC1 (PubMed:15340059). May also play a role in microtubule-mediated protein transport (By similarity). Also stimulates the intrinsic GTPase activity of the Ras-related proteins RAP1A and RAB5 (By similarity). {ECO:0000250|UniProtKB:P49816, ECO:0000269|PubMed:12271141, ECO:0000269|PubMed:15340059, ECO:0000269|PubMed:28215400}.; ","acmg|epilepsy|gedi|foundationOne|level2","[ \"Afatinib\" , \"Cetuximab\" , \"Everolimus\" , \"Sirolimus\" , \"Temsirolimus\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Everolimus\" , \"Sirolimus\" , \"Temsirolimus\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Everolimus\" , \"Sirolimus\" , \"Temsirolimus\"]","p.Arg1268Gly","c.3802C>G","MODERATE","1268/1807",31,1,{"$nulls":4},"5","695","810","525","604","637","729","0","0","0","0.3594",{"$nulls":20},"3.4786989999999998","-2.57;.;.;-2.95;.;-2.92;.;.;-2.95;-2.77;.;.;.;.;-2.93","2.255;.;.;.;.;.;.;.;.;2.255;.;.;.;.;.","0.999876","-2.39;.;.;-1.98;.;-1.95;.;.;-1.98;-1.98;.;.;.;.;-1.95","0.995;.;.;.;0.881;0.998;.;.;0.998;0.998;.;.;.;.;.","0.011;.;.;0.003;.;0.003;.;.;0.003;0.003;.;.;.;.;0.003","0.79;.;.;0.77;.;0.739;.;.;0.774;0.681;.;.;.;.;0.739",{"$nulls":3},"Unknown",-1,"AD","Tuberous sclerosis 2; Lymphangioleiomyomatosis ","Cardiovascular; Dental; Dermatologic; Neurologic; Oncologic; Ophthalmologic; Pulmonary; Renal","COSMIC,kMTOR,kP53,vpi3k,vpi3k,vpi3k","Mutations in this gene lead to tuberous sclerosis complex. Its gene product is believed to be a tumor suppressor and is able to stimulate specific GTPases. The protein associates with hamartin in a cytosolic complex, possibly acting as a chaperone for hamartin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008].",null,"C1860707| C0751674| C1846385","0/0","679,0","0","679","0/1","504,289","0.3644","793",null,"chr16:2081786:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3576"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TSC2","chr16:2081786","TSC2(R1268G)",null,null,"splice variant (In isoform 8. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Tuberous sclerosis 2 (TSC2) [MIM:613254]: An autosomal dominant multi-system disorder that affects especially the brain, kidneys, heart, and skin. It is characterized by hamartomas (benign overgrowths predominantly of a cell or tissue type that occurs normally in the organ) and hamartias (developmental abnormalities of tissue combination). Clinical manifestations include epilepsy, learning difficulties, behavioral problems, and skin lesions. Seizures can be intractable and premature death can occur from a variety of disease-associated causes. {ECO:0000269|PubMed:10069705, ECO:0000269|PubMed:10205261, ECO:0000269|PubMed:10533067, ECO:0000269|PubMed:10570911, ECO:0000269|PubMed:10607950, ECO:0000269|PubMed:10732801, ECO:0000269|PubMed:10735580, ECO:0000269|PubMed:12271141, ECO:0000269|PubMed:15024740, ECO:0000269|PubMed:15340059, ECO:0000269|PubMed:15595939, ECO:0000269|PubMed:15963462, ECO:0000269|PubMed:8824881, ECO:0000269|PubMed:9302281, ECO:0000269|PubMed:9463313, ECO:0000269|PubMed:9829910}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Lymphangioleiomyomatosis (LAM) [MIM:606690]: Progressive and often fatal lung disease characterized by a diffuse proliferation of abnormal smooth muscle cells in the lungs. It affects almost exclusively young women and can occur as an isolated disorder or in association with tuberous sclerosis complex. {ECO:0000269|PubMed:10823953, ECO:0000269|PubMed:11829138}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Focal cortical dysplasia 2 (FCORD2) [MIM:607341]: A form of focal cortical dysplasia, a malformation of cortical development that results in medically refractory epilepsy in the pediatric population and in adults. FCORD2 is a severe form, with onset usually in childhood, characterized by disrupted cortical lamination and specific cytological abnormalities. It is classified in 2 subtypes: type IIA characterized by dysmorphic neurons and lack of balloon cells; type IIB with dysmorphic neurons and balloon cells. {ECO:0000269|PubMed:28215400}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: In complex with TSC1, this tumor suppressor inhibits the nutrient-mediated or growth factor-stimulated phosphorylation of S6K1 and EIF4EBP1 by negatively regulating mTORC1 signaling (PubMed:12271141, PubMed:28215400). Acts as a GTPase-activating protein (GAP) for the small GTPase RHEB, a direct activator of the protein kinase activity of mTORC1 (PubMed:15340059). May also play a role in microtubule-mediated protein transport (By similarity). Also stimulates the intrinsic GTPase activity of the Ras-related proteins RAP1A and RAB5 (By similarity). {ECO:0000250|UniProtKB:P49816, ECO:0000269|PubMed:12271141, ECO:0000269|PubMed:15340059, ECO:0000269|PubMed:28215400}.; ","acmg|epilepsy|gedi|foundationOne|level2","[ \"Afatinib\" , \"Cetuximab\" , \"Everolimus\" , \"Sirolimus\" , \"Temsirolimus\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Everolimus\" , \"Sirolimus\" , \"Temsirolimus\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Everolimus\" , \"Sirolimus\" , \"Temsirolimus\"]","p.Arg1268Gly","c.3802C>G","MODERATE","1268/1807",31,1,{"$nulls":4},"5","695","632","525","469","639","560","0","0","0","0.7768",{"$nulls":20},"3.4786989999999998","-2.57;.;.;-2.95;.;-2.92;.;.;-2.95;-2.77;.;.;.;.;-2.93","2.255;.;.;.;.;.;.;.;.;2.255;.;.;.;.;.","0.999876","-2.39;.;.;-1.98;.;-1.95;.;.;-1.98;-1.98;.;.;.;.;-1.95","0.995;.;.;.;0.881;0.998;.;.;0.998;0.998;.;.;.;.;.","0.011;.;.;0.003;.;0.003;.;.;0.003;0.003;.;.;.;.;0.003","0.79;.;.;0.77;.;0.739;.;.;0.774;0.681;.;.;.;.;0.739",{"$nulls":3},"Unknown",-1,"AD","Tuberous sclerosis 2; Lymphangioleiomyomatosis ","Cardiovascular; Dental; Dermatologic; Neurologic; Oncologic; Ophthalmologic; Pulmonary; Renal","COSMIC,kMTOR,kP53,vpi3k,vpi3k,vpi3k","Mutations in this gene lead to tuberous sclerosis complex. Its gene product is believed to be a tumor suppressor and is able to stimulate specific GTPases. The protein associates with hamartin in a cytosolic complex, possibly acting as a chaperone for hamartin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008].",null,"C1860707| C0751674| C1846385","0/0","686,0","0","686","0/1","132,490","0.7878","622",null,"chr16:2081786:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.791"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TTC28","chr22:28163494","TTC28(S347A)",null,null,"repeat (TPR 7 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: During mitosis, may be involved in the condensation of spindle midzone microtubules, leading to the formation of midbody. {ECO:0000269|PubMed:23036704}.; ",{"$nulls":4},"p.Ser347Ala","c.1039T>G","MODERATE","347/2481",6,{"$nulls":5},"5","553","403","415","288","516","363","0","0","0","0.1818",{"$nulls":20},"2.126105",".;-3.17",".;-0.065","0.999985",".;-0.63",".;0.441",".;0.347",".;0.434",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","544,0","0","544","0/1","316,74","0.1897","390",null,"chr22:28163494:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1806"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TTLL3","chr3:9810356","TTLL3(P117L)",null,null,"splice variant (In isoform 4. ), splice variant (In isoform 2 and isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs371547801",0.0001943,null,"FUNCTION: Monoglycylase which modifies alpha- and beta-tubulin, generating side chains of glycine on the gamma-carboxyl groups of specific glutamate residues within the C-terminal tail of alpha- and beta-tubulin. Involved in the side-chain initiation step of the glycylation reaction by adding a single glycine chain to generate monoglycine side chains. Not involved in elongation step of the polyglycylation reaction. {ECO:0000269|PubMed:19524510}.; ",{"$nulls":4},"p.Pro117Leu","c.350C>T","MODERATE","117/915",1,{"$nulls":5},"5","65","97","45","73","55","82","0","0","0","0.1098",{"$nulls":20},"0.988668","3.56",null,"0.97538;1;0.699367;0.699367","-2.3",null,"0.023","0.058",{"$nulls":3},"ExAC_AF",0.0001943,{"$nulls":7},"0/0","59,0","0","59","0/1","80,8","0.0909","88",null,"chr3:9810356:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0959"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TTN","chr2:178597745","TTN(I19113F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Ile19113Phe","c.57337A>T","MODERATE","19113/35991",294,{"$nulls":5},"4","595","685","452","513","505","583","0","0","0","0.1424",{"$nulls":20},"3.2860110000000002","-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;.",".;.;.;0.605;.;.;0.605","0.999997;0.999984;0.999997;0.999997;0.999984;0.999978","-2.5;-2.63;.;.;-2.63;-2.63;.",".;.;.;0.994;.;.;0.994","0.176;0.178;.;.;0.339;0.319;.","0.556;0.671;0.444;0.435;0.671;0.633;0.422",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","589,0","0","589","0/1","574,90","0.1355","664",null,"chr2:178597745:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1442"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TTN","chr2:178597745","TTN(I19113F)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Ile19113Phe","c.57337A>T","MODERATE","19113/35991",294,{"$nulls":5},"4","595","331","452","244","505","283","0","0","0","0.3216",{"$nulls":20},"3.2860110000000002","-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;.",".;.;.;0.605;.;.;0.605","0.999997;0.999984;0.999997;0.999997;0.999984;0.999978","-2.5;-2.63;.;.;-2.63;-2.63;.",".;.;.;0.994;.;.;0.994","0.176;0.178;.;.;0.339;0.319;.","0.556;0.671;0.444;0.435;0.671;0.633;0.422",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","588,0","0","588","0/1","219,105","0.3241","324",null,"chr2:178597745:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3443"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","TTN","chr2:178723687","TTN(S7138Y)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Ser7138Tyr","c.21413C>A","MODERATE","7138/35991",74,1,{"$nulls":4},"5","281","350","216","275","266","316","0","0","0","0.1329",{"$nulls":20},"3.120328","-0.3;-0.3;-0.3;.",null,"1;1;1;0.949562;0.98489;0.949562","-3.22;.;.;.",".;.;0.999;0.999","0.105;.;.;.","0.411;0.39;0.437;0.432",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","278,0","0","278","0/1","303,50","0.1416","353",null,"chr2:178723687:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1418"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TTN","chr2:178723687","TTN(S7138Y)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Ser7138Tyr","c.21413C>A","MODERATE","7138/35991",74,1,{"$nulls":4},"5","281","164","216","126","265","144","0","0","0","0.3056",{"$nulls":20},"3.120328","-0.3;-0.3;-0.3;.",null,"1;1;1;0.949562;0.98489;0.949562","-3.22;.;.;.",".;.;0.999;0.999","0.105;.;.;.","0.411;0.39;0.437;0.432",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","278,0","0","278","0/1","112,53","0.3212","165",null,"chr2:178723687:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3095"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","TWIST1","chr7:19117118","TWIST1(Sequence Feature)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,"DISEASE: Robinow-Sorauf syndrome (RSS) [MIM:180750]: An autosomal dominant syndrome characterized by craniosynostosis, asymmetry of orbits, flat face, hypertelorism, a thin, long, and pointed nose, shallow orbits, strabismus, and broad great toes with a duplication of the distal phalanx. RSS is clinically similar to Saethre-Chotzen syndrome, with the most characteristic additional feature in Robinow-Sorauf syndrome being a bifid or partially duplicated hallux. {ECO:0000269|PubMed:10465122}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Craniosynostosis 1 (CRS1) [MIM:123100]: A primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. {ECO:0000269|PubMed:17343269}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Sweeney-Cox syndrome (SWCOS) [MIM:617746]: An autosomal dominant syndrome characterized by facial dysostosis, including hypertelorism, deficiencies of the eyelids and facial bones, cleft palate/velopharyngeal insufficiency, and low-set cupped ears. {ECO:0000269|PubMed:28369379}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Acts as a transcriptional regulator. Inhibits myogenesis by sequestrating E proteins, inhibiting trans-activation by MEF2, and inhibiting DNA-binding by MYOD1 through physical interaction. This interaction probably involves the basic domains of both proteins. Also represses expression of proinflammatory cytokines such as TNFA and IL1B. Regulates cranial suture patterning and fusion. Activates transcription as a heterodimer with E proteins. Regulates gene expression differentially, depending on dimer composition. Homodimers induce expression of FGFR2 and POSTN while heterodimers repress FGFR2 and POSTN expression and induce THBS1 expression. Heterodimerization is also required for osteoblast differentiation. Represses the activity of the circadian transcriptional activator: NPAS2-ARNTL/BMAL1 heterodimer (By similarity). {ECO:0000250|UniProtKB:P26687, ECO:0000269|PubMed:12553906, ECO:0000269|PubMed:25981568}.; ",{"$nulls":5},"c.204C>T","MODERATE",null,1,{"$nulls":5},"4","131","82","126","75",null,null,"0","0",{"$nulls":33},"Unknown",-1,"AD","Saethre-Chotzen syndrome; Robinow-Sorauf syndrome; Craniosynostosis, type 1","Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal ",null,"Basic helix-loop-helix (bHLH) transcription factors have been implicated in cell lineage determination and differentiation. The protein encoded by this gene is a bHLH transcription factor and shares similarity with another bHLH transcription factor, Dermo1. The strongest expression of this mRNA is in placental tissue; in adults, mesodermally derived tissues express this mRNA preferentially. Mutations in this gene have been found in patients with Saethre-Chotzen syndrome. [provided by RefSeq, Jul 2008].  ",null,"C4551902| C0175699| C1867146| C4540299","0/0","132,0","0","132","0/1","75,6","0.0741","81",null,"chr7:19117118:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.08"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","UBE2R2","chr9:33886930","UBE2R2(R76T)",null,null,"strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes monoubiquitination and 'Lys-48'-linked polyubiquitination. May be involved in degradation of katenin. {ECO:0000269|PubMed:12037680, ECO:0000269|PubMed:20061386}.; ",{"$nulls":4},"p.Arg76Thr","c.227G>C","MODERATE","76/238",2,{"$nulls":5},"5","613","636","409","412","557","544","0","0","0","0.318",{"$nulls":20},"3.419514","1.17","1.15","1","-4.14","0.464","0.048","0.636",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","588,1","0.0017","589","0/1","399,181","0.3121","580",null,"chr9:33886930:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3155"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","UBE2R2","chr9:33886930","UBE2R2(R76T)",null,null,"strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes monoubiquitination and 'Lys-48'-linked polyubiquitination. May be involved in degradation of katenin. {ECO:0000269|PubMed:12037680, ECO:0000269|PubMed:20061386}.; ",{"$nulls":4},"p.Arg76Thr","c.227G>C","MODERATE","76/238",2,{"$nulls":5},"5","613","328","409","212","558","297","0","0","0","0.6364",{"$nulls":20},"3.419514","1.17","1.15","1","-4.14","0.464","0.048","0.636",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","576,0","0","576","0/1","112,183","0.6203","295",null,"chr9:33886930:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6132"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","USPL1","chr13:30621816","USPL1(E51A)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: SUMO-specific isopeptidase involved in protein desumoylation. Specifically binds SUMO proteins with a higher affinity for SUMO2 and SUMO3 which it cleaves more efficiently. Also able to process full-length SUMO proteins to their mature forms (PubMed:22878415). Plays a key role in RNA polymerase-II- mediated snRNA transcription in the Cajal bodies (PubMed:24413172). Is a component of complexes that can bind to U snRNA genes (PubMed:24413172). {ECO:0000269|PubMed:22878415, ECO:0000269|PubMed:24413172}.; ",{"$nulls":4},"p.Glu51Ala","c.152A>C","MODERATE","51/1092",3,{"$nulls":5},"5","97","109","58","70","81","95","0","0","0","0.2526",{"$nulls":20},"1.295557","3.22","1.245","0.994844","-1.72","0.005","0.443","0.213",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","95,0","0","95","0/1","82,27","0.2477","109",null,"chr13:30621816:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2714"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","USPL1","chr13:30621816","USPL1(E51A)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: SUMO-specific isopeptidase involved in protein desumoylation. Specifically binds SUMO proteins with a higher affinity for SUMO2 and SUMO3 which it cleaves more efficiently. Also able to process full-length SUMO proteins to their mature forms (PubMed:22878415). Plays a key role in RNA polymerase-II- mediated snRNA transcription in the Cajal bodies (PubMed:24413172). Is a component of complexes that can bind to U snRNA genes (PubMed:24413172). {ECO:0000269|PubMed:22878415, ECO:0000269|PubMed:24413172}.; ",{"$nulls":4},"p.Glu51Ala","c.152A>C","MODERATE","51/1092",3,{"$nulls":5},"5","97","45","58","28","81","36","0","0","0","0.5",{"$nulls":20},"1.295557","3.22","1.245","0.994844","-1.72","0.005","0.443","0.213",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","95,0","0","95","0/1","21,22","0.5116","43",null,"chr13:30621816:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5357"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","VIT","chr2:36781750","VIT(G276R)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Promotes matrix assembly and cell adhesiveness. Plays a role in spinal cord formation by regulating the proliferation and differentiation of neural stem cells. {ECO:0000250|UniProtKB:Q8VHI5}.; ",{"$nulls":4},"p.Gly276Arg","c.826G>C","MODERATE","276/693",10,{"$nulls":5},"4","443","597","300","399","398","539","0.0023","0.0023","0","0.1707",{"$nulls":20},"1.6865480000000002","-0.27;-0.1",null,"0.888021;0.888021;1;1;1;1","-1.26;-1.67","0.018;.","0.255;0.144","0.18;0.23",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","428,0","0","428","0/1","448,109","0.1957","557",null,"chr2:36781750:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.188"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","VIT","chr2:36781750","VIT(G276R)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 5. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Promotes matrix assembly and cell adhesiveness. Plays a role in spinal cord formation by regulating the proliferation and differentiation of neural stem cells. {ECO:0000250|UniProtKB:Q8VHI5}.; ",{"$nulls":4},"p.Gly276Arg","c.826G>C","MODERATE","276/693",10,{"$nulls":5},"4","443","363","300","248","396","318","0.0023","0.0023","0","0.2799",{"$nulls":20},"1.6865480000000002","-0.27;-0.1",null,"0.888021;0.888021;1;1;1;1","-1.26;-1.67","0.018;.","0.255;0.144","0.18;0.23",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","430,0","0","430","0/1","242,102","0.2965","344",null,"chr2:36781750:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2984"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","XRN1","chr3:142421083","XRN1(Y369F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Major 5'-3' exoribonuclease involved in mRNA decay. Required for the 5'-3'-processing of the G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNA tetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (By similarity). Plays a role in replication-dependent histone mRNA degradation. May act as a tumor suppressor protein in osteogenic sarcoma (OGS). {ECO:0000250|UniProtKB:P97789, ECO:0000269|PubMed:18172165}.; ",{"$nulls":4},"p.Tyr369Phe","c.1106A>T","MODERATE","369/1706",10,{"$nulls":5},"5","262","374","154","222","243","332","0","0","0","0.1867",{"$nulls":20},"3.209156","1.51;1.51;.","1.965","1","-1.17;-1.17;-1.33","0.81;0.94;0.413","0.213;0.195;0.627","0.619;0.637;0.671",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","245,0","0","245","0/1","267,71","0.2101","338",null,"chr3:142421083:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1982"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","XRN1","chr3:142421083","XRN1(Y369F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Major 5'-3' exoribonuclease involved in mRNA decay. Required for the 5'-3'-processing of the G4 tetraplex-containing DNA and RNA substrates. The kinetic of hydrolysis is faster for G4 RNA tetraplex than for G4 DNA tetraplex and monomeric RNA tetraplex. Binds to RNA and DNA (By similarity). Plays a role in replication-dependent histone mRNA degradation. May act as a tumor suppressor protein in osteogenic sarcoma (OGS). {ECO:0000250|UniProtKB:P97789, ECO:0000269|PubMed:18172165}.; ",{"$nulls":4},"p.Tyr369Phe","c.1106A>T","MODERATE","369/1706",10,{"$nulls":5},"5","262","238","154","145","240","215","0","0","0","0.3209",{"$nulls":20},"3.209156","1.51;1.51;.","1.965","1","-1.17;-1.17;-1.33","0.81;0.94;0.413","0.213;0.195;0.627","0.619;0.637;0.671",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","256,0","0","256","0/1","158,73","0.316","231",null,"chr3:142421083:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3172"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZAN","chr7:100766639","ZAN(D1529Y)",{"$nulls":6},255,"PASS","Missense","rs370874509",2.3986567522187578E-4,null,"FUNCTION: Binds in a species-specific manner to the zona pellucida of the egg. May be involved in gamete recognition and/or signaling.; ",{"$nulls":4},"p.Asp1529Tyr","c.4585G>T","MODERATE","1529/2812",24,{"$nulls":5},"5","456","452","326","312","432","414","0","0","0","0.0894",{"$nulls":20},"2.291672",".;.;.;3.21","2.64","1",".;.;.;-5.91","0.995;.;0.995;.",null,"0.369;0.392;0.396;0.376",{"$nulls":3},"ESP6500_EA_AF",2.3986567522187578E-4,{"$nulls":7},"0/0","459,0","0","459","0/1","395,44","0.1002","439",null,"chr7:100766639:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1026"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZC2HC1A","chr8:78717419","ZC2HC1A(E302L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu302Leu","c.904_905delGAinsTT","MODERATE","302/325",9,{"$nulls":5},"4","330","413","229","276","280","333","0","0","0","0.0631",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","316,0","0","316","0/1","361,27","0.0696","388",null,"chr8:78717419:GA:TT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0725"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZC3H12A","chr1:37481693","ZC3H12A(D226Y)",null,null,"region of interest (RNase ), metal ion-binding site (Magnesium), mutagenesis site (Loss of pre-miRNA RNase activity, IL17A mRNA instability and antiviral effects; when associated with A-225. Loss of IL1B mRNA instability; when associated with N-141. ZC3H12A(D226A)), helix ","metal-binding-site:Magnesium","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Note=Increased expression of ZC3H12A is associated with ischemic heart disease (PubMed:16574901). {ECO:0000269|PubMed:16574901}.; ","FUNCTION: Endoribonuclease involved in various biological functions such as cellular inflammatory response and immune homeostasis, glial differentiation of neuroprogenitor cells, cell death of cardiomyocytes, adipogenesis and angiogenesis. Functions as an endoribonuclease involved in mRNA decay (PubMed:19909337). Modulates the inflammatory response by promoting the degradation of a set of translationally active cytokine-induced inflammation- related mRNAs, such as IL6 and IL12B, during the early phase of inflammation (PubMed:26320658). Prevents aberrant T-cell-mediated immune reaction by degradation of multiple mRNAs controlling T- cell activation, such as those encoding cytokines (IL6 and IL2), cell surface receptors (ICOS, TNFRSF4 and TNFR2) and transcription factor (REL) (By similarity). Inhibits cooperatively with ZC3H12A the differentiation of helper T cells Th17 in lungs. They repress target mRNA encoding the Th17 cell-promoting factors IL6, ICOS, REL, IRF4, NFKBID and NFKBIZ. The cooperation requires RNA-binding by RC3H1 and the nuclease activity of ZC3H12A (By similarity). Self regulates by destabilizing its own mRNA (By similarity). Cleaves mRNA harboring a stem-loop (SL), often located in their 3'-UTRs, during the early phase of inflammation in a helicase UPF1-dependent manner (PubMed:19909337, PubMed:26320658, PubMed:26134560, PubMed:22561375). Plays a role in the inhibition of microRNAs (miRNAs) biogenesis (PubMed:22055188). Cleaves the terminal loop of a set of precursor miRNAs (pre-miRNAs) important for the regulation of the inflammatory response leading to their degradation, and thus preventing the biosynthesis of mature miRNAs (PubMed:22055188). Plays also a role in promoting angiogenesis in response to inflammatory cytokines by inhibiting the production of antiangiogenic microRNAs via its anti-dicer RNase activity (PubMed:24048733). Affects the overall ubiquitination of cellular proteins (By similarity). Positively regulates deubiquitinase activity promoting the cleavage at 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains on TNF receptor-associated factors (TRAFs), preventing JNK and NF-kappa-B signaling pathway activation, and hence negatively regulating macrophage-mediated inflammatory response and immune homeostasis (By similarity). Induces also deubiquitination of the transcription factor HIF1A, probably leading to its stabilization and nuclear import, thereby positively regulating the expression of proangiogenic HIF1A- targeted genes (PubMed:24048733). Involved in a TANK-dependent negative feedback response to attenuate NF-kappaB activation through the deubiquitination of IKBKG or TRAF6 in response to interleukin-1-beta (IL1B) stimulation or upon DNA damage (PubMed:25861989). Prevents stress granule (SGs) formation and promotes macrophage apoptosis under stress conditions, including arsenite-induced oxidative stress, heat shock and energy deprivation (By similarity). Plays a role in the regulation of macrophage polarization; promotes IL4-induced polarization of macrophages M1 into anti-inflammatory M2 state (By similarity). May also act as a transcription factor that regulates the expression of multiple genes involved in inflammatory response, angiogenesis, adipogenesis and apoptosis (PubMed:16574901, PubMed:18364357). Functions as a positive regulator of glial differentiation of neuroprogenitor cells through an amyloid precursor protein (APP)-dependent signaling pathway (PubMed:19185603). Attenuates septic myocardial contractile dysfunction in response to lipopolysaccharide (LPS) by reducing I- kappa-B-kinase (IKK)-mediated NF-kappa-B activation, and hence myocardial proinflammatory cytokine production (By similarity). {ECO:0000250|UniProtKB:Q5D1E7, ECO:0000269|PubMed:16574901, ECO:0000269|PubMed:18364357, ECO:0000269|PubMed:19185603, ECO:0000269|PubMed:19909337, ECO:0000269|PubMed:22055188, ECO:0000269|PubMed:22561375, ECO:0000269|PubMed:24048733, ECO:0000269|PubMed:25861989, ECO:0000269|PubMed:26134560, ECO:0000269|PubMed:26320658}.; FUNCTION: (Microbial infection) Exhibits antiviral activity against HIV-1 in lymphocytes by decreasing the abundance of HIV-1 viral RNA species. {ECO:0000269|PubMed:24191027}.; ",{"$nulls":4},"p.Asp226Tyr","c.676G>T","MODERATE","226/599",4,{"$nulls":5},"5","695","702","514","503","619","624","0","0","0","0.1218",{"$nulls":20},"4.435326","-0.17;.","3.105;.","1","-8.93;.","1.0;.","0.0;.","0.974;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","679,0","0","679","0/1","579,83","0.1254","662",null,"chr1:37481693:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1233"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZC3H15","chr2:186504059","ZC3H15(E188K)",null,null,"zinc finger region (C3H1-type 2 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Protects DRG1 from proteolytic degradation. {ECO:0000250}.; ",{"$nulls":4},"p.Glu188Lys","c.562G>A","MODERATE","188/426",6,{"$nulls":5},"5","503","874","382","641","388","710","0","0","0","0.1141",{"$nulls":20},"4.9824","0.87","3.34","1","-3.48","1.0",null,"0.911",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","490,0","0","490","0/1","758,85","0.1008","843",null,"chr2:186504059:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1014"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ZC3H15","chr2:186504059","ZC3H15(E188K)",null,null,"zinc finger region (C3H1-type 2 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Protects DRG1 from proteolytic degradation. {ECO:0000250}.; ",{"$nulls":4},"p.Glu188Lys","c.562G>A","MODERATE","188/426",6,{"$nulls":5},"5","503","386","382","281","388","313","0","0","0","0.1917",{"$nulls":20},"4.9824","0.87","3.34","1","-3.48","1.0",null,"0.911",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","488,0","0","488","0/1","305,67","0.1801","372",null,"chr2:186504059:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1886"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZFHX4","chr8:76706496","ZFHX4(Q804_L809del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: May play a role in neural and muscle differentiation (By similarity). May be involved in transcriptional regulation. {ECO:0000250}.; ",{"$nulls":4},"p.Gln804_Leu809del","c.2412_2429delGATCCAGCATAATCTGCA","MODERATE","804/3616",2,{"$nulls":5},"4","516","575","386","420","429","475","0","0","0","0.0737",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C1867438","0/0","559,0","0","559","0/1","538,43","0.074","581",null,"chr8:76706496:AGCAGATCCAGCATAATCT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0786"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZIC4","chr3:147396350","ZIC4(R114C)",{"$nulls":6},255,"PASS","Missense","rs1006876526",-1,null,"FUNCTION: Binds to DNA. {ECO:0000250}.; ",{"$nulls":4},"p.Arg114Cys","c.340C>T","MODERATE","114/384",3,{"$nulls":5},"5","293","336","248","271","270","303","0","0","0","0.2244",{"$nulls":20},"4.045259","1.06;1.06;1.06;1.06;1.06;1.06;.;.","2.86;.;.;2.86;2.86;.;.;.",null,"-6.27;-6.3;-6.3;-6.27;-6.27;-6.19;-7.33;-7.94","0.998;.;.;0.998;0.998;.;.;.","0.0","0.696;0.715;0.694;0.693;0.692;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","294,0","0","294","0/1","257,77","0.2305","334",null,"chr3:147396350:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2435"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ZIC4","chr3:147396350","ZIC4(R114C)",{"$nulls":6},255,"PASS","Missense","rs1006876526",-1,null,"FUNCTION: Binds to DNA. {ECO:0000250}.; ",{"$nulls":4},"p.Arg114Cys","c.340C>T","MODERATE","114/384",3,{"$nulls":5},"5","293","267","248","224","270","235","0","0","0","0.417",{"$nulls":20},"4.045259","1.06;1.06;1.06;1.06;1.06;1.06;.;.","2.86;.;.;2.86;2.86;.;.;.",null,"-6.27;-6.3;-6.3;-6.27;-6.27;-6.19;-7.33;-7.94","0.998;.;.;0.998;0.998;.;.;.","0.0","0.696;0.715;0.694;0.693;0.692;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","294,0","0","294","0/1","153,108","0.4138","261",null,"chr3:147396350:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3839"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF182","chrX:47977084","ZNF182(V335L)",null,null,"zinc finger region (C2H2-type 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Val335Leu","c.1003G>C","MODERATE","335/639",7,{"$nulls":5},"4","177","178","154","163",null,null,"0","0",{"$nulls":22},"1.285299","2.24",".;0.085","0.999974;0.999986;0.999986","-0.92;-0.91",".;0.005","0.385;0.675","0.146;0.133",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","179,0","0","179","0/1","167,11","0.0618","178",null,"chrX:47977084:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0552"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF24","chr18:35340283","ZNF24(E121fs)",null,null,"domain (SCAN box ), helix ","helix:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcription factor required for myelination of differentiated oligodendrocytes. Required for the conversion of oligodendrocytes from the premyelinating to the myelinating state. In the developing central nervous system (CNS), involved in the maintenance in the progenitor stage by promoting the cell cycle. Specifically binds to the 5'-TCAT-3' DNA sequence (By similarity). Has transcription repressor activity in vitro. {ECO:0000250, ECO:0000269|PubMed:10585455}.; ",{"$nulls":4},"p.Glu121fs","c.360_367delAGAGGAGG","HIGH","120/368",2,{"$nulls":5},"5","468","508","374","381","436","467","0","0","0","0.2762",{"$nulls":5},"(ZNF24|ENSG00000172466|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","483,0","0","483","0/1","368,129","0.2596","497",null,"chr18:35340283:GCCTCCTCT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2677"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ZNF24","chr18:35340283","ZNF24(E121fs)",null,null,"domain (SCAN box ), helix ","helix:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcription factor required for myelination of differentiated oligodendrocytes. Required for the conversion of oligodendrocytes from the premyelinating to the myelinating state. In the developing central nervous system (CNS), involved in the maintenance in the progenitor stage by promoting the cell cycle. Specifically binds to the 5'-TCAT-3' DNA sequence (By similarity). Has transcription repressor activity in vitro. {ECO:0000250, ECO:0000269|PubMed:10585455}.; ",{"$nulls":4},"p.Glu121fs","c.360_367delAGAGGAGG","HIGH","120/368",2,{"$nulls":5},"5","468","240","374","193","435","216","0","0","0","0.588",{"$nulls":5},"(ZNF24|ENSG00000172466|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","482,0","0","482","0/1","86,141","0.6211","227",null,"chr18:35340283:GCCTCCTCT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5389"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF292","chr6:87261640","ZNF292(D2671N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp2671Asn","c.8011G>A","MODERATE","2671/2723",8,{"$nulls":5},"5","216","225","164","158","187","189","0","0","0","0.0952",{"$nulls":20},"4.030802","2.49;2.51","2.36;.","0.997313","-2.27","1.0;.","0.004","0.79;0.827",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","215,0","0","215","0/1","200,19","0.0868","219",null,"chr6:87261640:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0949"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF454","chr5:178946914","ZNF454(P60S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Pro60Ser","c.178C>T","MODERATE","60/522",4,{"$nulls":5},"4","297","403","217","291",null,null,"0","0",{"$nulls":22},"1.392293","5.49","2.175","0.992561","-6.26","0.0","0.014","0.154;0.155",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","289,0","0","289","0/1","363,24","0.062","387",null,"chr5:178946914:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.055"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF623","chr8:143651014","ZNF623(K382_L386del)",null,null,"zinc finger region (C2H2-type 10 )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Lys382_Leu386del","c.1145_1159delAAGCTTTCTTTCTGA","MODERATE","382/536",1,{"$nulls":5},"3",null,null,"254","260","227","240",null,null,"0","0.0583",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","339,0","0","339","0/1","321,19","0.0559","340",null,"chr8:143651014:GGAAAGCTTTCTTTCT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0692"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF639","chr3:179333112","ZNF639(A98V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds DNA and may function as a transcriptional repressor. {ECO:0000269|PubMed:16182284}.; ",{"$nulls":4},"p.Ala98Val","c.293C>T","MODERATE","98/485",6,{"$nulls":5},"5","414","598","281","382","371","526","0","0","0","0.1065",{"$nulls":20},"1.527995","3.91;.;.;3.91;4.59;3.91;.;.","0;.;.;0;.;0;.;0","0.99993","0.02;-1.24;-1.51;0.02;0.05;0.02;-1.52;.","0.0;.;.;0.0;.;0.0;.;0.0","0.437;0.41;0.337;0.437;0.414;0.437;0.339;.","0.097;.;.;0.1;.;0.098;.;0.1",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","405,0","0","405","0/1","495,68","0.1208","563",null,"chr3:179333112:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1178"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ZNF639","chr3:179333112","ZNF639(A98V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds DNA and may function as a transcriptional repressor. {ECO:0000269|PubMed:16182284}.; ",{"$nulls":4},"p.Ala98Val","c.293C>T","MODERATE","98/485",6,{"$nulls":5},"5","414","337","281","229","371","286","0","0","0","0.4301",{"$nulls":20},"1.527995","3.91;.;.;3.91;4.59;3.91;.;.","0;.;.;0;.;0;.;0","0.99993","0.02;-1.24;-1.51;0.02;0.05;0.02;-1.52;.","0.0;.;.;0.0;.;0.0;.;0.0","0.437;0.41;0.337;0.437;0.414;0.437;0.339;.","0.097;.;.;0.1;.;0.098;.;0.1",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","405,0","0","405","0/1","174,146","0.4562","320",null,"chr3:179333112:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4323"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ZNF668","chr16:31061085","ZNF668(E638K)",{"$nulls":6},255,"PASS","Missense","rs1363119018",-1,null,"FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.; ",{"$nulls":4},"p.Glu638Lys","c.1912G>A","MODERATE","638/642",4,{"$nulls":5},"4","247","193",null,null,"175","138","0","0","0","0.2681",{"$nulls":20},"2.37223","3.16;3.15;3.16;3.16;3.16;3.15",null,"0.989456","-1.16;-1.32;-1.16;-1.16;-1.16;-1.32",null,"0.028;0.026;0.028;0.028;0.028;0.026","0.37;0.48;0.369;0.36;0.37;0.478",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","243,0","0","243","0/1","148,37","0.2","185",null,"chr16:31061085:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZNF831","chr20:59191779","ZNF831(L254I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu254Ile","c.760C>A","MODERATE","254/1677",1,{"$nulls":5},"4","683","910","541","674","590","763","0","0","0","0.059",{"$nulls":20},"0.279926",".;3.46","1.525","1",".;-0.77","0.252",".;0.045",".;0.127",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","671,0","0","671","0/1","821,48","0.0552","869",null,"chr20:59191779:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0549"]
["10LD","T11","JLPIKTOR_JLPIKTOR_17113010LD","ZSCAN10","chr16:3090377","ZSCAN10(G353R)",null,null,"zinc finger region (C2H2-type 3 )",{"$nulls":3},255,"PASS","Missense","rs1187420282",-1,null,"FUNCTION: Embryonic stem (ES) cell-specific transcription factor required to maintain ES cell pluripotency. Can both activate and /or repress expression of target genes, depending on the context. Specifically binds the 5'-[GA]CGCNNGCG[CT]-3' DNA consensus sequence. Regulates expression of POU5F1/OCT4, ZSCAN4 and ALYREF/THOC4. {ECO:0000250|UniProtKB:Q3URR7}.; ",{"$nulls":4},"p.Gly353Arg","c.1057G>A","MODERATE","353/780",6,{"$nulls":5},"5","461","450","378","366","390","377","0","0","0","0.374",{"$nulls":20},"2.764137",".;0.28;0.28",".;1.925;.","0.996145;0.992914;1",".;-5.09;.",".;1.0;.",".;0.002;.","0.657;0.664;0.559",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","451,0","0","451","0/1","276,167","0.377","443",null,"chr16:3090377:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3689"]
["10LD","T10","JLPIKTOR_JLPIKTOR_17113010LD","ZSCAN10","chr16:3090377","ZSCAN10(G353R)",null,null,"zinc finger region (C2H2-type 3 )",{"$nulls":3},255,"PASS","Missense","rs1187420282",-1,null,"FUNCTION: Embryonic stem (ES) cell-specific transcription factor required to maintain ES cell pluripotency. Can both activate and /or repress expression of target genes, depending on the context. Specifically binds the 5'-[GA]CGCNNGCG[CT]-3' DNA consensus sequence. Regulates expression of POU5F1/OCT4, ZSCAN4 and ALYREF/THOC4. {ECO:0000250|UniProtKB:Q3URR7}.; ",{"$nulls":4},"p.Gly353Arg","c.1057G>A","MODERATE","353/780",6,{"$nulls":5},"5","461","357","378","296","390","293","0","0","0","0.7577",{"$nulls":20},"2.764137",".;0.28;0.28",".;1.925;.","0.996145;0.992914;1",".;-5.09;.",".;1.0;.",".;0.002;.","0.657;0.664;0.559",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","452,0","0","452","0/1","86,266","0.7557","352",null,"chr16:3090377:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113010LD","somatic","somatic","JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113010LD/somatic/JLPIKTOR_17113010LD_1_PB_WBC_C8_A3S7X-JLPIKTOR_17113010LD_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7568"]

{"sheet":"11JZ","index":8,"n_rows":289,"n_cols":107,"rows_kept":289}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ABCA2","chr9:137013928","ABCA2(A1481T)",null,null,"sequence variant (Found in a patient with epilepsy, concomitant developmental delay and microcephalia; unknown pathological significance. )",{"$nulls":3},255,"PASS","Missense","rs1220666029",-1,null,"FUNCTION: Probable transporter, its natural substrate has not been found yet. May have a role in macrophage lipid metabolism and neural development.; ",{"$nulls":4},"p.Ala1481Thr","c.4441G>A","MODERATE","1481/2466",28,{"$nulls":5},"4","1326","850","974","606","1161","739","0","0","0","0.0825",{"$nulls":20},"3.426347","-3.77;-3.77;-3.77;.",".;1.7;.;.","0.999896","-1.39;-1.39;-1.39;.",".;0.999;.;.","0.141;0.142;0.146;.","0.709;0.701;0.708;0.701",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN263395","0/0","1288,0","0","1288","0/1","758,67","0.0812","825",null,"chr9:137013928:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0743"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ABCA2","chr9:137013928","ABCA2(A1481T)",null,null,"sequence variant (Found in a patient with epilepsy, concomitant developmental delay and microcephalia; unknown pathological significance. )",{"$nulls":3},255,"PASS","Missense","rs1220666029",-1,null,"FUNCTION: Probable transporter, its natural substrate has not been found yet. May have a role in macrophage lipid metabolism and neural development.; ",{"$nulls":4},"p.Ala1481Thr","c.4441G>A","MODERATE","1481/2466",28,{"$nulls":5},"4","1326","741","974","526","1162","657","0","0","0","0.0837",{"$nulls":20},"3.426347","-3.77;-3.77;-3.77;.",".;1.7;.;.","0.999896","-1.39;-1.39;-1.39;.",".;0.999;.;.","0.141;0.142;0.146;.","0.709;0.701;0.708;0.701",{"$nulls":3},"Unknown",-1,{"$nulls":6},"CN263395","0/0","1265,0","0","1265","0/1","645,58","0.0825","703",null,"chr9:137013928:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0837"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ACHE","chr7:100893511","ACHE(G241D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis. {ECO:0000269|PubMed:11985878, ECO:0000269|PubMed:1517212, ECO:0000269|PubMed:1748670, ECO:0000269|PubMed:2714437}.; ",{"$nulls":4},"p.Gly241Asp","c.722G>A","MODERATE","241/617",2,{"$nulls":5},"5","728","615","626","518","613","512","0","0","0","0.0781",{"$nulls":20},"3.205512","-0.24","2.03;2.03;2.03;2.03;2.03;.;.;2.03","1","-3.16;-3.69;-3.16;-2.99;-3.16;-3.77;-3.51;-2.99","1.0;1.0;1.0;1.0;1.0;.;.;1.0","0.031;0.104;0.031;0.059;0.031;0.017;0.06;0.059","0.807;0.777;0.807;0.807;0.789;.;.;0.808",{"$nulls":3},"Unknown",-1,"BG","Blood group, Yt system","Hematologic",{"$nulls":3},"C1862189","0/0","715,0","0","715","0/1","541,49","0.0831","590",null,"chr7:100893511:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0734"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ACHE","chr7:100893511","ACHE(G241D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis. {ECO:0000269|PubMed:11985878, ECO:0000269|PubMed:1517212, ECO:0000269|PubMed:1748670, ECO:0000269|PubMed:2714437}.; ",{"$nulls":4},"p.Gly241Asp","c.722G>A","MODERATE","241/617",2,{"$nulls":5},"5","728","570","626","486","612","483","0","0","0","0.087",{"$nulls":20},"3.205512","-0.24","2.03;2.03;2.03;2.03;2.03;.;.;2.03","1","-3.16;-3.69;-3.16;-2.99;-3.16;-3.77;-3.51;-2.99","1.0;1.0;1.0;1.0;1.0;.;.;1.0","0.031;0.104;0.031;0.059;0.031;0.017;0.06;0.059","0.807;0.777;0.807;0.807;0.789;.;.;0.808",{"$nulls":3},"Unknown",-1,"BG","Blood group, Yt system","Hematologic",{"$nulls":3},"C1862189","0/0","716,0","0","716","0/1","513,51","0.0904","564",null,"chr7:100893511:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0947"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ACTN4","chr19:38729125","ACTN4(A850T)",{"$nulls":6},255,"PASS","Missense","rs376869655",1.1627906976744188E-4,"DISEASE: Focal segmental glomerulosclerosis 1 (FSGS1) [MIM:603278]: A renal pathology defined by the presence of segmental sclerosis in glomeruli and resulting in proteinuria, reduced glomerular filtration rate and progressive decline in renal function. Renal insufficiency often progresses to end-stage renal disease, a highly morbid state requiring either dialysis therapy or kidney transplantation. {ECO:0000269|PubMed:10700177, ECO:0000269|PubMed:18164029, ECO:0000269|PubMed:18436095, ECO:0000269|PubMed:22351778, ECO:0000269|PubMed:22732337, ECO:0000269|PubMed:23014460, ECO:0000269|PubMed:23890478}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein (Probable). Probably involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation (PubMed:15772161). Involved in tight junction assembly in epithelial cells probably through interaction with MICALL2. Links MICALL2 to the actin cytoskeleton and recruits it to the tight junctions (By similarity). May also function as a transcriptional coactivator, stimulating transcription mediated by the nuclear hormone receptors PPARG and RARA (PubMed:22351778). {ECO:0000250|UniProtKB:P57780, ECO:0000269|PubMed:15772161, ECO:0000269|PubMed:22351778, ECO:0000305|PubMed:9508771}.; ",{"$nulls":4},"p.Ala850Thr","c.2548G>A","MODERATE","850/911",20,1,{"$nulls":4},"4","708","673","500","476","646","589","0","0","0","0.0798",{"$nulls":20},"3.598773","0.89","2.565;.;.;.","0.999986;0.999998;0.99999","-0.83;-0.98;-1.02;-1.89","0.918;.;.;.","0.096;0.245;0.288;0.091","0.735;0.715;0.765;.",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,"AD","Focal segmental glomerulosclerosis 1","Renal",{"$nulls":3},"C4551527","0/0","693,0","0","693","0/1","586,57","0.0886","643",null,"chr19:38729125:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0819"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ACTN4","chr19:38729125","ACTN4(A850T)",{"$nulls":6},255,"PASS","Missense","rs376869655",1.1627906976744188E-4,"DISEASE: Focal segmental glomerulosclerosis 1 (FSGS1) [MIM:603278]: A renal pathology defined by the presence of segmental sclerosis in glomeruli and resulting in proteinuria, reduced glomerular filtration rate and progressive decline in renal function. Renal insufficiency often progresses to end-stage renal disease, a highly morbid state requiring either dialysis therapy or kidney transplantation. {ECO:0000269|PubMed:10700177, ECO:0000269|PubMed:18164029, ECO:0000269|PubMed:18436095, ECO:0000269|PubMed:22351778, ECO:0000269|PubMed:22732337, ECO:0000269|PubMed:23014460, ECO:0000269|PubMed:23890478}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein (Probable). Probably involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation (PubMed:15772161). Involved in tight junction assembly in epithelial cells probably through interaction with MICALL2. Links MICALL2 to the actin cytoskeleton and recruits it to the tight junctions (By similarity). May also function as a transcriptional coactivator, stimulating transcription mediated by the nuclear hormone receptors PPARG and RARA (PubMed:22351778). {ECO:0000250|UniProtKB:P57780, ECO:0000269|PubMed:15772161, ECO:0000269|PubMed:22351778, ECO:0000305|PubMed:9508771}.; ",{"$nulls":4},"p.Ala850Thr","c.2548G>A","MODERATE","850/911",20,1,{"$nulls":4},"4","708","548","500","390","647","475","0","0","0","0.0842",{"$nulls":20},"3.598773","0.89","2.565;.;.;.","0.999986;0.999998;0.99999","-0.83;-0.98;-1.02;-1.89","0.918;.;.;.","0.096;0.245;0.288;0.091","0.735;0.715;0.765;.",{"$nulls":3},"ESP6500_EA_AF",1.1627906976744188E-4,"AD","Focal segmental glomerulosclerosis 1","Renal",{"$nulls":3},"C4551527","0/0","692,0","0","692","0/1","478,44","0.0843","522",null,"chr19:38729125:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1026"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ACTR1B","chr2:97658096","ACTR1B(A258S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a multi-subunit complex involved in microtubule based vesicle motility. It is associated with the centrosome.; ",{"$nulls":4},"p.Ala258Ser","c.772G>T","MODERATE","258/376",8,{"$nulls":5},"5","773","585","589","436","671","505","0","0","0","0.0891",{"$nulls":20},"3.035679","-3.48","2.665","0.999998","-2.89","0.989","0.004","0.684",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","764,0","0","764","0/1","519,53","0.0927","572",null,"chr2:97658096:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0894"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ACTR1B","chr2:97658096","ACTR1B(A258S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a multi-subunit complex involved in microtubule based vesicle motility. It is associated with the centrosome.; ",{"$nulls":4},"p.Ala258Ser","c.772G>T","MODERATE","258/376",8,{"$nulls":5},"5","773","493","589","374","672","436","0","0","0","0.0894",{"$nulls":20},"3.035679","-3.48","2.665","0.999998","-2.89","0.989","0.004","0.684",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","763,0","0","763","0/1","435,45","0.0938","480",null,"chr2:97658096:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0909"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ACVR1C","chr2:157538630","ACVR1C(K433N)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine protein kinase which forms a receptor complex on ligand binding. The receptor complex consisting of 2 type II and 2 type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators, SMAD2 and SMAD3. Receptor for activin AB, activin B and NODAL. Plays a role in cell differentiation, growth arrest and apoptosis. {ECO:0000269|PubMed:12063393, ECO:0000269|PubMed:15531507}.; ","level2",{"$nulls":3},"p.Lys433Asn","c.1299G>T","MODERATE","433/493",8,{"$nulls":5},"4","550","523","361","343","491","463","0.0018","0.0018","0","0.0518",{"$nulls":20},"2.719338","-0.21","2.1;.;.;.","0.999928","-4.28;-4.36;-4.3;-4.3","0.863;.;0.955;0.598","0.002;0.002;0.002;0.001","0.416;0.484;0.532;0.561",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","515,2","0.0039","517","0/1","446,30","0.063","476",null,"chr2:157538630:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0641"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ACVR1C","chr2:157538630","ACVR1C(K433N)",null,null,"topological domain (Cytoplasmic ), domain (Protein kinase )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Serine/threonine protein kinase which forms a receptor complex on ligand binding. The receptor complex consisting of 2 type II and 2 type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators, SMAD2 and SMAD3. Receptor for activin AB, activin B and NODAL. Plays a role in cell differentiation, growth arrest and apoptosis. {ECO:0000269|PubMed:12063393, ECO:0000269|PubMed:15531507}.; ","level2",{"$nulls":3},"p.Lys433Asn","c.1299G>T","MODERATE","433/493",8,{"$nulls":5},"4","550","427","361","294","492","387","0.0018","0.0018","0","0.093",{"$nulls":20},"2.719338","-0.21","2.1;.;.;.","0.999928","-4.28;-4.36;-4.3;-4.3","0.863;.;0.955;0.598","0.002;0.002;0.002;0.001","0.416;0.484;0.532;0.561",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","516,2","0.0039","518","0/1","352,34","0.0881","386",null,"chr2:157538630:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0986"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ADAMTS16","chr5:5303327","ADAMTS16(R950H)",null,null,"domain (TSP type-1 3 ), disulfide bond , disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs764367334",1.516E-4,{"$nulls":6},"p.Arg950His","c.2849G>A","MODERATE","950/1224",19,1,{"$nulls":4},"4","567","365","449","274","485","313","0","0","0","0.0767",{"$nulls":20},"3.817514","-1.42","4.55","0.999967","-4.35","1.0",null,"0.972",{"$nulls":3},"ExAC_EAS_AF",1.516E-4,{"$nulls":7},"0/0","566,0","0","566","0/1","330,24","0.0678","354",null,"chr5:5303327:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0657"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ADH1A","chr4:99286854","ADH1A(E75_K85del)",null,null,"strand ",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Glu75_Lys85del","c.222_254delGGAGAGTGTTGGAGAAGGGGTGACTACAGTCAA","MODERATE","74/375",3,{"$nulls":5},"4",null,null,"277","200","401","272",null,null,"0","0.0735",{"$nulls":31},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the alcohol dehydrogenase family. The encoded protein is the alpha subunit of class I alcohol dehydrogenase, which consists of several homo- and heterodimers of alpha, beta and gamma subunits. Alcohol dehydrogenases catalyze the oxidation of alcohols to aldehydes. This gene is active in the liver in early fetal life but only weakly active in adult liver. This gene is found in a cluster with six additional alcohol dehydrogenase genes, including those encoding the beta and gamma subunits, on the long arm of chromosome 4. Mutations in this gene may contribute to variation in certain personality traits and substance dependence. [provided by RefSeq, Nov 2010].  ",null,null,"0/0","509,0","0","509","0/1","341,23","0.0632","364",null,"chr4:99286854:TTTGACTGTAGTCACCCCTTCTCCAACACTCTCC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ADH1A","chr4:99286854","ADH1A(E75_K85del)",null,null,"strand ",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,{"$nulls":6},"p.Glu75_Lys85del","c.222_254delGGAGAGTGTTGGAGAAGGGGTGACTACAGTCAA","MODERATE","74/375",3,{"$nulls":5},"4",null,null,"277","182","401","275",null,null,"0","0.0909",{"$nulls":31},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the alcohol dehydrogenase family. The encoded protein is the alpha subunit of class I alcohol dehydrogenase, which consists of several homo- and heterodimers of alpha, beta and gamma subunits. Alcohol dehydrogenases catalyze the oxidation of alcohols to aldehydes. This gene is active in the liver in early fetal life but only weakly active in adult liver. This gene is found in a cluster with six additional alcohol dehydrogenase genes, including those encoding the beta and gamma subunits, on the long arm of chromosome 4. Mutations in this gene may contribute to variation in certain personality traits and substance dependence. [provided by RefSeq, Nov 2010].  ",null,null,"0/0","509,0","0","509","0/1","327,24","0.0684","351",null,"chr4:99286854:TTTGACTGTAGTCACCCCTTCTCCAACACTCTCC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1154"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","AEBP1","chr7:44110808","AEBP1(M495T)",null,null,"domain (F5/8 type C ), region of interest (Required for DNA-binding and interaction with NFKBIA ), region of interest (Interaction with MAPK1 and MAPK3 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs772566263",9.862e-05,"DISEASE: Ehlers-Danlos syndrome, classic-like, 2 (EDSCLL2) [MIM:618000]: A variant form of Ehlers-Danlos syndrome, a connective tissue disorder. EDSCLL2 patients show severe joint and skin laxity, osteoporosis affecting the hips and spine, osteoarthritis, soft redundant skin that can be acrogeria-like, delayed wound healing with abnormal atrophic scarring, and shoulder, hip, knee, and ankle dislocations. Additional variable features include gastrointestinal and genitourinary manifestations (bowel rupture, gut dysmotility, cryptorchidism, and hernias), vascular complications (mitral valve prolapse and aortic root dilation), and skeletal anomalies. EDSCLL2 inheritance is autosomal recessive. {ECO:0000269|PubMed:27023906, ECO:0000269|PubMed:29606302}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 1: As a positive regulator of collagen fibrillogenesis, it is probably involved in the organization and remodeling of the extracellualr matrix. {ECO:0000269|PubMed:29606302}.; ",{"$nulls":4},"p.Met495Thr","c.1484T>C","MODERATE","495/1158",12,{"$nulls":5},"4","772","752","605","562","676","656","0","0","0","0.0564",{"$nulls":20},"4.567452","-4.29","1.775","0.999176;0.767935","-1.66","0.958","0.002","0.56",{"$nulls":3},"ExAC_SAS_AF",9.862e-05,{"$nulls":6},"C4693870","0/0","751,0","0","751","0/1","672,40","0.0562","712",null,"chr7:44110808:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0587"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","AEBP1","chr7:44110808","AEBP1(M495T)",null,null,"domain (F5/8 type C ), region of interest (Required for DNA-binding and interaction with NFKBIA ), region of interest (Interaction with MAPK1 and MAPK3 ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs772566263",9.862e-05,"DISEASE: Ehlers-Danlos syndrome, classic-like, 2 (EDSCLL2) [MIM:618000]: A variant form of Ehlers-Danlos syndrome, a connective tissue disorder. EDSCLL2 patients show severe joint and skin laxity, osteoporosis affecting the hips and spine, osteoarthritis, soft redundant skin that can be acrogeria-like, delayed wound healing with abnormal atrophic scarring, and shoulder, hip, knee, and ankle dislocations. Additional variable features include gastrointestinal and genitourinary manifestations (bowel rupture, gut dysmotility, cryptorchidism, and hernias), vascular complications (mitral valve prolapse and aortic root dilation), and skeletal anomalies. EDSCLL2 inheritance is autosomal recessive. {ECO:0000269|PubMed:27023906, ECO:0000269|PubMed:29606302}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Isoform 1: As a positive regulator of collagen fibrillogenesis, it is probably involved in the organization and remodeling of the extracellualr matrix. {ECO:0000269|PubMed:29606302}.; ",{"$nulls":4},"p.Met495Thr","c.1484T>C","MODERATE","495/1158",12,{"$nulls":5},"4","772","683","605","520","674","598","0","0","0","0.0803",{"$nulls":20},"4.567452","-4.29","1.775","0.999176;0.767935","-1.66","0.958","0.002","0.56",{"$nulls":3},"ExAC_SAS_AF",9.862e-05,{"$nulls":6},"C4693870","0/0","750,0","0","750","0/1","604,50","0.0765","654",null,"chr7:44110808:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0769"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","AFAP1L2","chr10:114299374","AFAP1L2(R667G)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in a signaling cascade by enhancing the kinase activity of SRC. Contributes to SRC-regulated transcription activation. {ECO:0000269|PubMed:17412687}.; ",{"$nulls":4},"p.Arg667Gly","c.1999C>G","MODERATE","667/818",16,{"$nulls":5},"4","292","213","190","143","272","193","0","0","0","0.0518",{"$nulls":20},"3.947362","2.13","2.99","0.999539","-6.57","1.0","0.001","0.741;0.766",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","278,0","0","278","0/1","194,11","0.0537","205",null,"chr10:114299374:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0699"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","AFAP1L2","chr10:114299374","AFAP1L2(R667G)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in a signaling cascade by enhancing the kinase activity of SRC. Contributes to SRC-regulated transcription activation. {ECO:0000269|PubMed:17412687}.; ",{"$nulls":4},"p.Arg667Gly","c.1999C>G","MODERATE","667/818",16,{"$nulls":5},"4","292","221","190","147","271","203","0","0","0","0.1034",{"$nulls":20},"3.947362","2.13","2.99","0.999539","-6.57","1.0","0.001","0.741;0.766",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","270,0","0","270","0/1","182,26","0.125","208",null,"chr10:114299374:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1156"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","AGRP","chr16:67483031","AGRP(L70F)",null,null,"propeptide ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Obesity (OBESITY) [MIM:601665]: A condition characterized by an increase of body weight beyond the limitation of skeletal and physical requirements, as the result of excessive accumulation of body fat. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in weight homeostasis. Involved in the control of feeding behavior through the central melanocortin system. Acts as alpha melanocyte-stimulating hormone antagonist by inhibiting cAMP production mediated by stimulation of melanocortin receptors within the hypothalamus and adrenal gland. Has very low activity with MC5R (By similarity). Is an inverse agonist for MC3R and MC4R being able to suppress their constitutive activity. It promotes MC3R and MC4R endocytosis in an arrestin-dependent manner. {ECO:0000250, ECO:0000269|PubMed:10371151, ECO:0000269|PubMed:11145747, ECO:0000269|PubMed:15927146, ECO:0000269|PubMed:17041250, ECO:0000269|PubMed:9892020}.; ",{"$nulls":4},"p.Leu70Phe","c.210G>T","MODERATE","70/132",3,{"$nulls":5},"5","658","563","477","394","572","493","0","0","0","0.0669",{"$nulls":20},"3.060256","1.11","2.705","0.995109","-0.57","0.999","0.016","0.27",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes an antagonist of the melanocortin-3 and melanocortin-4 receptor. It appears to regulate hypothalamic control of feeding behavior via melanocortin receptor and/or intracellular calcium regulation, and thus plays a role in weight homeostasis. Mutations in this gene have been associated with late on-set obesity. [provided by RefSeq, Dec 2009].  ",null,"C0028754","0/0","629,0","0","629","0/1","475,36","0.0705","511",null,"chr16:67483031:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0685"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","AGRP","chr16:67483031","AGRP(L70F)",null,null,"propeptide ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Obesity (OBESITY) [MIM:601665]: A condition characterized by an increase of body weight beyond the limitation of skeletal and physical requirements, as the result of excessive accumulation of body fat. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in weight homeostasis. Involved in the control of feeding behavior through the central melanocortin system. Acts as alpha melanocyte-stimulating hormone antagonist by inhibiting cAMP production mediated by stimulation of melanocortin receptors within the hypothalamus and adrenal gland. Has very low activity with MC5R (By similarity). Is an inverse agonist for MC3R and MC4R being able to suppress their constitutive activity. It promotes MC3R and MC4R endocytosis in an arrestin-dependent manner. {ECO:0000250, ECO:0000269|PubMed:10371151, ECO:0000269|PubMed:11145747, ECO:0000269|PubMed:15927146, ECO:0000269|PubMed:17041250, ECO:0000269|PubMed:9892020}.; ",{"$nulls":4},"p.Leu70Phe","c.210G>T","MODERATE","70/132",3,{"$nulls":5},"5","658","419","477","295","568","371","0","0","0","0.0809",{"$nulls":20},"3.060256","1.11","2.705","0.995109","-0.57","0.999","0.016","0.27",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes an antagonist of the melanocortin-3 and melanocortin-4 receptor. It appears to regulate hypothalamic control of feeding behavior via melanocortin receptor and/or intracellular calcium regulation, and thus plays a role in weight homeostasis. Mutations in this gene have been associated with late on-set obesity. [provided by RefSeq, Dec 2009].  ",null,"C0028754","0/0","629,0","0","629","0/1","358,37","0.0937","395",null,"chr16:67483031:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0712"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","AKNA","chr9:114347765","AKNA(R1119Q)",null,null,"DNA-binding region (A.T hook ), splice variant (In isoform 6. ), splice variant (In isoform 3. ), sequence variant (In dbSNP:rs3748178. AKNA(R1119Q))",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that specifically activates the expression of the CD40 receptor and its ligand CD40L/CD154, two cell surface molecules on lymphocytes that are critical for antigen-dependent-B-cell development. Binds to A/T-rich promoters. {ECO:0000269|PubMed:11268217}.; ",{"$nulls":4},"p.Arg1119Gln","c.3356_3357delGGinsAA","MODERATE","1119/1439",16,{"$nulls":5},"3",null,null,"85","69","52","47",null,null,"0","0.1489",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","101,0","0","101","0/1","79,9","0.1023","88",null,"chr9:114347765:CC:TT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1014"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ANGPTL6","chr19:10094844","ANGPTL6(P226R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the wound healing process. May promote epidermal proliferation, remodeling and regeneration. May promote the chemotactic activity of endothelial cells and induce neovascularization. May counteract high-fat diet-induced obesity and related insulin resistance through increased energy expenditure.; ",{"$nulls":4},"p.Pro226Arg","c.677C>G","MODERATE","226/470",3,{"$nulls":5},"5","389","393","279","268","366","347","0","0","0","0.0749",{"$nulls":20},"1.3741940000000001","0.34;0.69;0.69",".;1.04;1.04","0.998618",".;.;0.4",".;0.001;0.001",".;.;0.385","0.178;0.135;0.133",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","379,0","0","379","0/1","345,28","0.0751","373",null,"chr19:10094844:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0896"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ANGPTL6","chr19:10094844","ANGPTL6(P226R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in the wound healing process. May promote epidermal proliferation, remodeling and regeneration. May promote the chemotactic activity of endothelial cells and induce neovascularization. May counteract high-fat diet-induced obesity and related insulin resistance through increased energy expenditure.; ",{"$nulls":4},"p.Pro226Arg","c.677C>G","MODERATE","226/470",3,{"$nulls":5},"4","389","328","279","227","366","298","0","0","0","0.0604",{"$nulls":20},"1.3741940000000001","0.34;0.69;0.69",".;1.04;1.04","0.998618",".;.;0.4",".;0.001;0.001",".;.;0.385","0.178;0.135;0.133",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","380,0","0","380","0/1","302,19","0.0592","321",null,"chr19:10094844:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0617"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ANKRD30A","chr10:37219197","ANKRD30A(S1225F)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser1225Phe","c.3674C>T","MODERATE","1225/1460",40,{"$nulls":5},"3","345","254",{"$nulls":4},"0","0",{"$nulls":22},"0.412607",".;2.66;2.66;2.66","0.405;.;.;.","1",".;-0.85;-0.49;.","0.004;.;.;.",".;0.842;0.94;.","0.096;0.098;0.081;0.102",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","344,0","0","344","0/1","231,14","0.0571","245",null,"chr10:37219197:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ANKRD42","chr11:83211319","ANKRD42(E159K)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu159Lys","c.475G>A","MODERATE","159/527",5,{"$nulls":5},"4","364","276","298","214","284","217","0.0055","0.0055","0","0.0876",{"$nulls":20},"2.577349","0.68;-1.6;-0.04;0.68;2.41;2.41;2.41",".;.;.;.;.;0.065;.","0.941697;0.941697;0.966389;0.941697;0.966389;0.966389;0.966389","-1.7;-1.68;-1.51;-1.7;-1.54;-1.52;-1.58","0.622;.;.;.;.;0.673;0.768","0.074;0.162;0.5;0.091;0.483;0.368;0.33","0.353;0.276;0.325;0.342;0.351;0.291;0.334",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","352,2","0.0056","354","0/1","245,21","0.0789","266",null,"chr11:83211319:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0748"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ANKS3","chr16:4726706","ANKS3(Q148H)",null,null,"repeat (ANK 4 ), region of interest (Interaction with NEK7 )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln148His","c.444G>C","MODERATE","148/656",5,{"$nulls":5},"5","399","354","306","259","341","313","0","0","0","0.0735",{"$nulls":20},"2.492029",".;-0.09;0.65;0.65;-0.5;-0.5","0.18;.;0.18;.;.;.","0.999991;0.999997;0.999997;1",".;-1.6;-1.67;.;.;.","0.998;.;0.998;.;.;.",".;0.022;0.053;.;.;.","0.691;0.764;0.714;0.705;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","391,0","0","391","0/1","301,27","0.0823","328",null,"chr16:4726706:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0695"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","APMAP","chr20:24973711","APMAP(G119C)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Exhibits strong arylesterase activity with beta-naphthyl acetate and phenyl acetate. May play a role in adipocyte differentiation. {ECO:0000269|PubMed:18513186}.; ",{"$nulls":4},"p.Gly119Cys","c.355G>T","MODERATE","119/416",4,{"$nulls":5},"5","688","615","468","420","599","538","0","0","0","0.0651",{"$nulls":20},"4.039793","1.01","3.74","1","-7.9","1.0",null,"0.979",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","661,0","0","661","0/1","557,42","0.0701","599",null,"chr20:24973711:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0714"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ARHGAP15","chr2:143768074","ARHGAP15(E444*)",null,null,"domain (Rho-GAP ), strand ","beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function","rs747712329",6.058e-05,null,"FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction. {ECO:0000269|PubMed:12650940}.; ",{"$nulls":4},"p.Glu444*","c.1330G>T","HIGH","444/475",14,{"$nulls":5},"3",null,null,"261","250","343","317",null,null,"0","0.0505",{"$nulls":20},"8.420327",null,null,"1",{"$nulls":3},"0.411",{"$nulls":3},"ExAC_SAS_AF",6.058e-05,{"$nulls":7},"0/0","380,0","0","380","0/1","338,18","0.0506","356",null,"chr2:143768074:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.06"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ARHGAP15","chr2:143768074","ARHGAP15(E444*)",null,null,"domain (Rho-GAP ), strand ","beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Loss Of Function","rs747712329",6.058e-05,null,"FUNCTION: GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. Has activity toward RAC1. Overexpression results in an increase in actin stress fibers and cell contraction. {ECO:0000269|PubMed:12650940}.; ",{"$nulls":4},"p.Glu444*","c.1330G>T","HIGH","444/475",14,{"$nulls":5},"5","391","318","261","222","344","284","0.0026","0.0026","0","0.0951",{"$nulls":20},"8.420327",null,null,"1",{"$nulls":3},"0.411",{"$nulls":3},"ExAC_SAS_AF",6.058e-05,{"$nulls":7},"0/0","367,1","0.0027","368","0/1","266,41","0.1336","307",null,"chr2:143768074:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1306"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ARID5B","chr10:62069736","ARID5B(E380Q)",null,null,"domain (ARID ), splice variant (In isoform 3. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Defects in ARID5B may be a cause of susceptibility to coronary atherosclerosis in the Japanese population.; DISEASE: Leukemia, acute lymphoblastic (ALL) [MIM:613065]: A subtype of acute leukemia, a cancer of the white blood cells. ALL is a malignant disease of bone marrow and the most common malignancy diagnosed in children. The malignant cells are lymphoid precursor cells (lymphoblasts) that are arrested in an early stage of development. The lymphoblasts replace the normal marrow elements, resulting in a marked decrease in the production of normal blood cells. Consequently, anemia, thrombocytopenia, and neutropenia occur to varying degrees. The lymphoblasts also proliferate in organs other than the marrow, particularly the liver, spleen, and lymphnodes. {ECO:0000269|PubMed:19684603, ECO:0000269|PubMed:19684604, ECO:0000269|PubMed:20042726, ECO:0000269|PubMed:20054350, ECO:0000269|PubMed:20189245, ECO:0000269|PubMed:20460642, ECO:0000269|PubMed:21098271}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Transcription coactivator that binds to the 5'-AATA[CT]- 3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2- ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer. {ECO:0000269|PubMed:21532585}.; ","gedi",{"$nulls":3},"p.Glu380Gln","c.1138G>C","MODERATE","380/1188",8,{"$nulls":5},"5","345","274","257","195","298","239","0","0","0","0.0837",{"$nulls":20},"4.095746","-0.09","1.1;.","1","-2.09;-2.06","0.878;0.872","0.034;0.016","0.688;0.711",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","326,0","0","326","0/1","242,24","0.0902","266",null,"chr10:62069736:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0872"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ARID5B","chr10:62069736","ARID5B(E380Q)",null,null,"domain (ARID ), splice variant (In isoform 3. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Defects in ARID5B may be a cause of susceptibility to coronary atherosclerosis in the Japanese population.; DISEASE: Leukemia, acute lymphoblastic (ALL) [MIM:613065]: A subtype of acute leukemia, a cancer of the white blood cells. ALL is a malignant disease of bone marrow and the most common malignancy diagnosed in children. The malignant cells are lymphoid precursor cells (lymphoblasts) that are arrested in an early stage of development. The lymphoblasts replace the normal marrow elements, resulting in a marked decrease in the production of normal blood cells. Consequently, anemia, thrombocytopenia, and neutropenia occur to varying degrees. The lymphoblasts also proliferate in organs other than the marrow, particularly the liver, spleen, and lymphnodes. {ECO:0000269|PubMed:19684603, ECO:0000269|PubMed:19684604, ECO:0000269|PubMed:20042726, ECO:0000269|PubMed:20054350, ECO:0000269|PubMed:20189245, ECO:0000269|PubMed:20460642, ECO:0000269|PubMed:21098271}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Transcription coactivator that binds to the 5'-AATA[CT]- 3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2- ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer. {ECO:0000269|PubMed:21532585}.; ","gedi",{"$nulls":3},"p.Glu380Gln","c.1138G>C","MODERATE","380/1188",8,{"$nulls":5},"5","345","250","257","174","300","224","0","0","0","0.1161",{"$nulls":20},"4.095746","-0.09","1.1;.","1","-2.09;-2.06","0.878;0.872","0.034;0.016","0.688;0.711",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","325,0","0","325","0/1","204,30","0.1282","234",null,"chr10:62069736:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1207"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ARPC5","chr1:183630610","ARPC5(V85L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation- promoting factor (NPF) (PubMed:9230079). The Arp2/3 complex mediates the formation of branched actin networks in the cytoplasm, providing the force for cell motility (PubMed:9230079). In addition to its role in the cytoplasmic cytoskeleton, the Arp2/3 complex also promotes actin polymerization in the nucleus, thereby regulating gene transcription and repair of damaged DNA (PubMed:29925947). The Arp2/3 complex promotes homologous recombination (HR) repair in response to DNA damage by promoting nuclear actin polymerization, leading to drive motility of double- strand breaks (DSBs) (PubMed:29925947). {ECO:0000269|PubMed:29925947, ECO:0000269|PubMed:9230079}.; ",{"$nulls":4},"p.Val85Leu","c.253G>T","MODERATE","85/154",3,{"$nulls":5},"4","244","198",null,null,"227","188","0","0","0","0.0851",{"$nulls":20},"3.904948",null,"2.9;.;.","1","-2.75;-2.85;-2.75","0.994;.;.","0.069;0.002;0.069","0.762;0.764;0.716",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","239,0","0","239","0/1","177,16","0.0829","193",null,"chr1:183630610:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ASPM","chr1:197101675","ASPM(N2526Y)",null,null,"splice variant (In isoform 2. ), sequence variant (In dbSNP:rs587783267. ASPM(N2526D))",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Microcephaly 5, primary, autosomal recessive (MCPH5) [MIM:608716]: A disease defined as a head circumference more than 3 standard deviations below the age-related mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Despite this marked reduction in size, the gyral pattern is relatively well preserved, with no major abnormality in cortical architecture. Affected individuals are mentally retarded. Primary microcephaly is further defined by the absence of other syndromic features or significant neurological deficits due to degenerative brain disorder. {ECO:0000269|PubMed:12355089, ECO:0000269|PubMed:14574646, ECO:0000269|PubMed:22989186}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in mitotic spindle regulation and coordination of mitotic processes. The function in regulating microtubule dynamics at spindle poles including spindle orientation, astral microtubule density and poleward microtubule flux seems to depend on the association with the katanin complex formed by KATNA1 and KATNB1. Enhances the microtubule lattice severing activity of KATNA1 by recruiting the katanin complex to microtubules. Can block microtubule minus-end growth and reversely this function can be enhanced by the katanin complex (PubMed:28436967). May have a preferential role in regulating neurogenesis. {ECO:0000269|PubMed:12355089, ECO:0000269|PubMed:15972725, ECO:0000269|PubMed:28436967}.; ",{"$nulls":4},"p.Asn2526Tyr","c.7576A>T","MODERATE","2526/3477",18,{"$nulls":5},"5","240","249","182","188","218","215","0","0","0","0.1535",{"$nulls":20},"1.711191","-0.7","2.42","1","-1.79","0.988","0.021","0.303",{"$nulls":3},"Unknown",-1,"AR","Microcephaly, primary autosomal recessive, 5","Neurologic",{"$nulls":3},"C1837501","0/0","239,0","0","239","0/1","209,35","0.1434","244",null,"chr1:197101675:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1277"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ASPM","chr1:197101675","ASPM(N2526Y)",null,null,"splice variant (In isoform 2. ), sequence variant (In dbSNP:rs587783267. ASPM(N2526D))",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Microcephaly 5, primary, autosomal recessive (MCPH5) [MIM:608716]: A disease defined as a head circumference more than 3 standard deviations below the age-related mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Despite this marked reduction in size, the gyral pattern is relatively well preserved, with no major abnormality in cortical architecture. Affected individuals are mentally retarded. Primary microcephaly is further defined by the absence of other syndromic features or significant neurological deficits due to degenerative brain disorder. {ECO:0000269|PubMed:12355089, ECO:0000269|PubMed:14574646, ECO:0000269|PubMed:22989186}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in mitotic spindle regulation and coordination of mitotic processes. The function in regulating microtubule dynamics at spindle poles including spindle orientation, astral microtubule density and poleward microtubule flux seems to depend on the association with the katanin complex formed by KATNA1 and KATNB1. Enhances the microtubule lattice severing activity of KATNA1 by recruiting the katanin complex to microtubules. Can block microtubule minus-end growth and reversely this function can be enhanced by the katanin complex (PubMed:28436967). May have a preferential role in regulating neurogenesis. {ECO:0000269|PubMed:12355089, ECO:0000269|PubMed:15972725, ECO:0000269|PubMed:28436967}.; ",{"$nulls":4},"p.Asn2526Tyr","c.7576A>T","MODERATE","2526/3477",18,{"$nulls":5},"5","240","246","182","191","218","207","0","0","0","0.2464",{"$nulls":20},"1.711191","-0.7","2.42","1","-1.79","0.988","0.021","0.303",{"$nulls":3},"Unknown",-1,"AR","Microcephaly, primary autosomal recessive, 5","Neurologic",{"$nulls":3},"C1837501","0/0","239,0","0","239","0/1","182,58","0.2417","240",null,"chr1:197101675:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2356"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ATAD2","chr8:123347098","ATAD2(D736H)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.; ",{"$nulls":4},"p.Asp736His","c.2206G>C","MODERATE","736/1390",16,1,{"$nulls":4},"5","382","372","317","310","316","298","0","0","0","0.1376",{"$nulls":20},"1.777079","-2.93;1.48","-0.11;.","0.999976;0.999944","-0.77;-0.67","0.0;.","0.103;0.177","0.115;0.074",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","380,0","0","380","0/1","316,46","0.1271","362",null,"chr8:123347098:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1355"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ATAD2","chr8:123347098","ATAD2(D736H)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional coactivator of the nuclear receptor ESR1 required to induce the expression of a subset of estradiol target genes, such as CCND1, MYC and E2F1. May play a role in the recruitment or occupancy of CREBBP at some ESR1 target gene promoters. May be required for histone hyperacetylation. Involved in the estrogen-induced cell proliferation and cell cycle progression of breast cancer cells. {ECO:0000269|PubMed:17998543}.; ",{"$nulls":4},"p.Asp736His","c.2206G>C","MODERATE","736/1390",16,1,{"$nulls":4},"5","382","399","317","328","316","318","0","0","0","0.173",{"$nulls":20},"1.777079","-2.93;1.48","-0.11;.","0.999976;0.999944","-0.77;-0.67","0.0;.","0.103;0.177","0.115;0.074",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","379,0","0","379","0/1","337,55","0.1403","392",null,"chr8:123347098:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1433"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","AVPR2","chrX:153906394","AVPR2(W296*)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Diabetes insipidus, nephrogenic, X-linked (XNDI) [MIM:304800]: A disorder caused by the inability of the renal collecting ducts to absorb water in response to arginine vasopressin. Characterized by excessive water drinking (polydipsia), excessive urine excretion (polyuria), persistent hypotonic urine, and hypokalemia. {ECO:0000269|PubMed:10694923, ECO:0000269|PubMed:10770218, ECO:0000269|PubMed:11026555, ECO:0000269|PubMed:11232028, ECO:0000269|PubMed:11916004, ECO:0000269|PubMed:1303257, ECO:0000269|PubMed:1303271, ECO:0000269|PubMed:1356229, ECO:0000269|PubMed:16845277, ECO:0000269|PubMed:7560098, ECO:0000269|PubMed:7833930, ECO:0000269|PubMed:7984150, ECO:0000269|PubMed:7987330, ECO:0000269|PubMed:7999078, ECO:0000269|PubMed:8037205, ECO:0000269|PubMed:8045948, ECO:0000269|PubMed:8078903, ECO:0000269|PubMed:8267567, ECO:0000269|PubMed:8479490, ECO:0000269|PubMed:8514744, ECO:0000269|PubMed:9402087, ECO:0000269|PubMed:9452109, ECO:0000269|PubMed:9711877}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor for arginine vasopressin. The activity of this receptor is mediated by G proteins which activate adenylate cyclase. Involved in renal water reabsorption. {ECO:0000269|PubMed:19440390}.; ",{"$nulls":4},"p.Trp296*","c.888G>A","HIGH","296/371",2,{"$nulls":5},"4","728","547","580","431",null,null,"0","0",{"$nulls":22},"7.675162",null,null,"1",{"$nulls":3},".;0.913;0.914;0.837",{"$nulls":3},"Unknown",-1,"XL","Diabetes insipidus, nephrogenic, X-linked","Endocrine; Renal",{"$nulls":3},"C1845202| C1563705","0/0","717,0","0","717","0/1","498,32","0.0604","530",null,"chrX:153906394:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.051"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","AVPR2","chrX:153906394","AVPR2(W296*)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Diabetes insipidus, nephrogenic, X-linked (XNDI) [MIM:304800]: A disorder caused by the inability of the renal collecting ducts to absorb water in response to arginine vasopressin. Characterized by excessive water drinking (polydipsia), excessive urine excretion (polyuria), persistent hypotonic urine, and hypokalemia. {ECO:0000269|PubMed:10694923, ECO:0000269|PubMed:10770218, ECO:0000269|PubMed:11026555, ECO:0000269|PubMed:11232028, ECO:0000269|PubMed:11916004, ECO:0000269|PubMed:1303257, ECO:0000269|PubMed:1303271, ECO:0000269|PubMed:1356229, ECO:0000269|PubMed:16845277, ECO:0000269|PubMed:7560098, ECO:0000269|PubMed:7833930, ECO:0000269|PubMed:7984150, ECO:0000269|PubMed:7987330, ECO:0000269|PubMed:7999078, ECO:0000269|PubMed:8037205, ECO:0000269|PubMed:8045948, ECO:0000269|PubMed:8078903, ECO:0000269|PubMed:8267567, ECO:0000269|PubMed:8479490, ECO:0000269|PubMed:8514744, ECO:0000269|PubMed:9402087, ECO:0000269|PubMed:9452109, ECO:0000269|PubMed:9711877}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor for arginine vasopressin. The activity of this receptor is mediated by G proteins which activate adenylate cyclase. Involved in renal water reabsorption. {ECO:0000269|PubMed:19440390}.; ",{"$nulls":4},"p.Trp296*","c.888G>A","HIGH","296/371",2,{"$nulls":5},"5","728","477","580","369","635","415","0","0","0","0.1181",{"$nulls":20},"7.675162",null,null,"1",{"$nulls":3},".;0.913;0.914;0.837",{"$nulls":3},"Unknown",-1,"XL","Diabetes insipidus, nephrogenic, X-linked","Endocrine; Renal",{"$nulls":3},"C1845202| C1563705","0/0","719,0","0","719","0/1","412,56","0.1197","468",null,"chrX:153906394:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.122"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","B3GAT3","chr11:62615765","B3GAT3(K315T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Multiple joint dislocations, short stature, and craniofacial dysmorphism with or without congenital heart defects (JDSCD) [MIM:245600]: An autosomal recessive disease characterized by dysmorphic facies, bilateral dislocations of the elbows, hips, and knees, clubfeet, and short stature, as well as cardiovascular defects. {ECO:0000269|PubMed:21763480, ECO:0000269|PubMed:24668659, ECO:0000269|PubMed:25893793, ECO:0000269|PubMed:26086840}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Glycosaminoglycans biosynthesis (PubMed:25893793). Involved in forming the linkage tetrasaccharide present in heparan sulfate and chondroitin sulfate. Transfers a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region trisaccharide Gal-beta-1,3-Gal-beta-1,4- Xyl covalently bound to a Ser residue at the glycosaminylglycan attachment site of proteoglycans. Can also play a role in the biosynthesis of l2/HNK-1 carbohydrate epitope on glycoproteins. Shows strict specificity for Gal-beta-1,3-Gal-beta-1,4-Xyl, exhibiting negligible incorporation into other galactoside substrates including Galbeta1-3Gal beta1-O-benzyl, Galbeta1- 4GlcNAc and Galbeta1-4Glc. Stimulates 2-phosphoxylose phosphatase activity of PXYLP1 in presence of uridine diphosphate-glucuronic acid (UDP-GlcUA) during completion of linkage region formation (PubMed:24425863). {ECO:0000269|PubMed:24425863, ECO:0000269|PubMed:25893793}.; ",{"$nulls":4},"p.Lys315Thr","c.944A>C","MODERATE","315/335",5,{"$nulls":5},"5","331","286","237","198","271","240","0","0","0","0.1083",{"$nulls":20},"3.182847","-1.05","2.025","1","-3.33","0.001","0.048","0.172",{"$nulls":3},"Unknown",-1,"AR","Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects","Cardiovascular; Craniofacial; Musculoskeletal",{"$nulls":3},"C3278404","0/0","327,0","0","327","0/1","252,29","0.1032","281",null,"chr11:62615765:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.096"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","B3GAT3","chr11:62615765","B3GAT3(K315T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Multiple joint dislocations, short stature, and craniofacial dysmorphism with or without congenital heart defects (JDSCD) [MIM:245600]: An autosomal recessive disease characterized by dysmorphic facies, bilateral dislocations of the elbows, hips, and knees, clubfeet, and short stature, as well as cardiovascular defects. {ECO:0000269|PubMed:21763480, ECO:0000269|PubMed:24668659, ECO:0000269|PubMed:25893793, ECO:0000269|PubMed:26086840}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Glycosaminoglycans biosynthesis (PubMed:25893793). Involved in forming the linkage tetrasaccharide present in heparan sulfate and chondroitin sulfate. Transfers a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region trisaccharide Gal-beta-1,3-Gal-beta-1,4- Xyl covalently bound to a Ser residue at the glycosaminylglycan attachment site of proteoglycans. Can also play a role in the biosynthesis of l2/HNK-1 carbohydrate epitope on glycoproteins. Shows strict specificity for Gal-beta-1,3-Gal-beta-1,4-Xyl, exhibiting negligible incorporation into other galactoside substrates including Galbeta1-3Gal beta1-O-benzyl, Galbeta1- 4GlcNAc and Galbeta1-4Glc. Stimulates 2-phosphoxylose phosphatase activity of PXYLP1 in presence of uridine diphosphate-glucuronic acid (UDP-GlcUA) during completion of linkage region formation (PubMed:24425863). {ECO:0000269|PubMed:24425863, ECO:0000269|PubMed:25893793}.; ",{"$nulls":4},"p.Lys315Thr","c.944A>C","MODERATE","315/335",5,{"$nulls":5},"5","331","209","237","150","273","162","0","0","0","0.1605",{"$nulls":20},"3.182847","-1.05","2.025","1","-3.33","0.001","0.048","0.172",{"$nulls":3},"Unknown",-1,"AR","Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects","Cardiovascular; Craniofacial; Musculoskeletal",{"$nulls":3},"C3278404","0/0","327,0","0","327","0/1","174,25","0.1256","199",null,"chr11:62615765:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.12"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","BRWD1","chr21:39313458","BRWD1(P12S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional activator. May be involved in chromatin remodeling (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape. {ECO:0000250, ECO:0000269|PubMed:21834987}.; ",{"$nulls":4},"p.Pro12Ser","c.34C>T","MODERATE","12/2320",1,{"$nulls":5},"5","229","237","161","155","178","165","0","0","0","0.3636",{"$nulls":20},"2.171945","0.76","-0.63","0.771556","-0.05;-0.09;0.08;-0.49","0.617;0.005;.;.","0.249;0.273;0.354;0.702","0.135;0.2;0.176;0.08",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","217,0","0","217","0/1","144,81","0.36","225",null,"chr21:39313458:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3548"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","BRWD1","chr21:39313458","BRWD1(P12S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be a transcriptional activator. May be involved in chromatin remodeling (By similarity). Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the control of cell shape. {ECO:0000250, ECO:0000269|PubMed:21834987}.; ",{"$nulls":4},"p.Pro12Ser","c.34C>T","MODERATE","12/2320",1,{"$nulls":5},"5","229","218","161","144","178","153","0","0","0","0.5033",{"$nulls":20},"2.171945","0.76","-0.63","0.771556","-0.05;-0.09;0.08;-0.49","0.617;0.005;.;.","0.249;0.273;0.354;0.702","0.135;0.2;0.176;0.08",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","217,0","0","217","0/1","104,100","0.4902","204",null,"chr21:39313458:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4861"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","C16orf74","chr16:85710297","C16orf74(M13I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Met13Ile","c.39G>T","MODERATE","13/76",3,{"$nulls":5},"4","389","368","270","245",null,null,"0","0",{"$nulls":22},"3.139348",null,null,"0.587694",".;.;-4.0",".;.;0.426",null,"0.586;0.872;0.541",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","386,0","0","386","0/1","330,20","0.0571","350",null,"chr16:85710297:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0531"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","C16orf74","chr16:85710297","C16orf74(M13I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Met13Ile","c.39G>T","MODERATE","13/76",3,{"$nulls":5},"4","391","373","270","245",null,null,"0","0",{"$nulls":22},"3.139348",null,null,"0.587694",".;.;-4.0",".;.;0.426",null,"0.586;0.872;0.541",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","383,0","0","383","0/1","323,22","0.0638","345",null,"chr16:85710297:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0571"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","C19orf52","chr19:10928838","C19orf52(L6V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu6Val","c.16C>G","MODERATE","6/260",1,{"$nulls":5},"4","614","533","419","355","510","431","0","0","0","0.0812",{"$nulls":20},"0.758054",null,null,"0.996552","-0.24","0.002","0.151","0.134",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","596,0","0","596","0/1","480,42","0.0805","522",null,"chr19:10928838:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0761"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","C19orf52","chr19:10928838","C19orf52(L6V)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Leu6Val","c.16C>G","MODERATE","6/260",1,{"$nulls":5},"4","614","457","419","297","513","370","0","0","0","0.1",{"$nulls":20},"0.758054",null,null,"0.996552","-0.24","0.002","0.151","0.134",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","594,0","0","594","0/1","400,43","0.0971","443",null,"chr19:10928838:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0842"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","C1orf100","chr1:244378631","C1orf100(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,{"$nulls":6},"p.Glu107_Ile108del","c.320_325+17delAGATTGGTAAGTCAGGCCAACTG","HIGH","107/147",4,{"$nulls":5},"4",null,null,"195","173","153","141",null,null,"0","0.0851",{"$nulls":5},"(C1orf100|ENSG00000173728|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","287,0","0","287","0/1","234,21","0.0824","255",null,"chr1:244378631:ATGAGATTGGTAAGTCAGGCCAAC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0578"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","C7orf43","chr7:100157887","C7orf43(T155S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr155Ser","c.463A>T","MODERATE","155/580",2,{"$nulls":5},"4","349","335","242","228",null,null,"0","0",{"$nulls":22},"2.442394","1.49","0.145","0.990231;1","-1.45","0.518","0.204","0.682",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","343,0","0","343","0/1","312,19","0.0574","331",null,"chr7:100157887:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0526"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","C7orf43","chr7:100157887","C7orf43(T155S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr155Ser","c.463A>T","MODERATE","155/580",2,{"$nulls":5},"4","349","284","242","201",null,null,"0","0",{"$nulls":22},"2.442394","1.49","0.145","0.990231;1","-1.45","0.518","0.204","0.682",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","342,0","0","342","0/1","249,28","0.1011","277",null,"chr7:100157887:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0945"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CACNA1H","chr16:1209123","CACNA1H(P1152L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Epilepsy, idiopathic generalized 6 (EIG6) [MIM:611942]: A disorder characterized by recurring generalized seizures in the absence of detectable brain lesions and/or metabolic abnormalities. Generalized seizures arise diffusely and simultaneously from both hemispheres of the brain. {ECO:0000269|PubMed:15048902}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Epilepsy, childhood absence 6 (ECA6) [MIM:611942]: A subtype of idiopathic generalized epilepsy characterized by an onset at age 6-7 years, frequent absence seizures (several per day) and bilateral, synchronous, symmetric 3-Hz spike waves on EEG. Tonic-clonic seizures often develop in adolescence. Absence seizures may either remit or persist into adulthood. {ECO:0000269|PubMed:12891677}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hyperaldosteronism, familial, 4 (HALD4) [MIM:617027]: A form of familial hyperaldosteronism, a disorder characterized by hypertension, elevated aldosterone levels despite low plasma renin activity, and abnormal adrenal steroid production. There is significant phenotypic heterogeneity, and some individuals never develop hypertension. {ECO:0000269|PubMed:25907736, ECO:0000269|PubMed:27729216}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Voltage-sensitive calcium channel that gives rise to T- type calcium currents. T-type calcium channels belong to the \"low- voltage activated (LVA)\" group. A particularity of this type of channel is an opening at quite negative potentials, and a voltage- dependent inactivation (PubMed:9670923, PubMed:9930755, PubMed:27149520). T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle (Probable). They may also be involved in the modulation of firing patterns of neurons (PubMed:15048902). In the adrenal zona glomerulosa, participates in the signaling pathway leading to aldosterone production in response to either AGT/angiotensin II, or hyperkalemia (PubMed:25907736, PubMed:27729216). {ECO:0000269|PubMed:25907736, ECO:0000269|PubMed:27149520, ECO:0000269|PubMed:27729216, ECO:0000269|PubMed:9670923, ECO:0000269|PubMed:9930755, ECO:0000305, ECO:0000305|PubMed:15048902}.; ","gedi|level2",{"$nulls":3},"p.Pro1152Leu","c.3455C>T","MODERATE","1152/2353",17,{"$nulls":5},"5","520","460","428","366","415","356","0","0","0","0.0815",{"$nulls":20},"3.695115","-2.92;.;-2.92;-2.92","2.74;.;2.74;2.74","0.999982","-7.56;.;-7.56;-7.56","0.958;.;1.0;1.0","0.001;.;0.001;0.001","0.697;.;0.7;0.641",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",null,null,"C2749872| C4310756","0/0","521,0","0","521","0/1","424,34","0.0742","458",null,"chr16:1209123:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0683"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CACNA1I","chr22:39649524","CACNA1I(L531fs)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This channel gives rise to T-type calcium currents. T-type calcium channels belong to the \"low-voltage activated (LVA)\" group and are strongly blocked by nickel and mibefradil. A particularity of this type of channels is an opening at quite negative potentials, and a voltage- dependent inactivation. T-type channels serve pacemaking functions in both central neurons and cardiac nodal cells and support calcium signaling in secretory cells and vascular smooth muscle. They may also be involved in the modulation of firing patterns of neurons which is important for information processing as well as in cell growth processes. Gates in voltage ranges similar to, but higher than alpha 1G or alpha 1H (By similarity). {ECO:0000250}.; ","level2",{"$nulls":3},"p.Leu531fs","c.1592_1593delTG","HIGH","531/2223",10,{"$nulls":5},"4",null,null,"154","155","182","193",null,null,"0","0.0518",{"$nulls":5},"(CACNA1I|ENSG00000100346|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","196,0","0","196","0/1","190,11","0.0547","201",null,"chr22:39649524:CTG:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0645"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","CACNA2D4","chr12:1858580","CACNA2D4(E669*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Retinal cone dystrophy 4 (RCD4) [MIM:610478]: Characterized by minimal symptoms except for slowly progressive reduction in visual acuity. {ECO:0000269|PubMed:17033974}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The alpha-2/delta subunit of voltage-dependent calcium channels regulates calcium current density and activation/inactivation kinetics of the calcium channel. {ECO:0000269|PubMed:12181424}.; ","level2",{"$nulls":3},"p.Glu669*","c.2005G>T","HIGH","669/1154",20,{"$nulls":5},"4","490","512","360","364","421","440","0","0","0","0.1545",{"$nulls":5},"(CACNA2D4|ENSG00000151062|1|1.00)","(CACNA2D4|ENSG00000151062|1|1.00)",{"$nulls":13},"9.796218",null,null,"1",{"$nulls":3},"0.407;0.413;0.422;0.411;0.409;0.37",{"$nulls":3},"Unknown",-1,"AR","Retinal cone dystrophy 4","Ophthalmologic","kMAPK",null,null,"C1864849","0/0","471,0","0","471","0/1","415,71","0.1461","486",null,"chr12:1858580:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1511"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CACNA2D4","chr12:1858580","CACNA2D4(E669*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Retinal cone dystrophy 4 (RCD4) [MIM:610478]: Characterized by minimal symptoms except for slowly progressive reduction in visual acuity. {ECO:0000269|PubMed:17033974}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The alpha-2/delta subunit of voltage-dependent calcium channels regulates calcium current density and activation/inactivation kinetics of the calcium channel. {ECO:0000269|PubMed:12181424}.; ","level2",{"$nulls":3},"p.Glu669*","c.2005G>T","HIGH","669/1154",20,{"$nulls":5},"4","490","465","360","322","422","387","0","0","0","0.2584",{"$nulls":5},"(CACNA2D4|ENSG00000151062|1|1.00)","(CACNA2D4|ENSG00000151062|1|1.00)",{"$nulls":13},"9.796218",null,null,"1",{"$nulls":3},"0.407;0.413;0.422;0.411;0.409;0.37",{"$nulls":3},"Unknown",-1,"AR","Retinal cone dystrophy 4","Ophthalmologic","kMAPK",null,null,"C1864849","0/0","459,0","0","459","0/1","329,107","0.2454","436",null,"chr12:1858580:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2516"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","CARD11","chr7:2937234","CARD11(A382T)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: B-cell expansion with NFKB and T-cell anergy (BENTA) [MIM:616452]: An autosomal dominant condition characterized by onset in infancy of splenomegaly and polyclonal expansion of B cells, resulting in peripheral lymphocytosis. Affected individuals also show mild immune dysfunction, including some defective antibody responses and T-cell anergy. There may be a predisposition to the development of B-cell malignancy. {ECO:0000269|PubMed:23129749, ECO:0000269|PubMed:28628108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Immunodeficiency 11 A (IMD11A) [MIM:615206]: An autosomal recessive primary immunodeficiency characterized by normal numbers of T and B-lymphocytes, but defective intracellular signaling. There is a block in B-cell differentiation with increased numbers of transitional B-cells and hypogammaglobulinemia, as well as decreased numbers of regulatory T-cells and defects in T-cell function. {ECO:0000269|PubMed:23374270, ECO:0000269|PubMed:23561803}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Immunodeficiency 11B with atopic dermatitis (IMD11B) [MIM:617638]: An autosomal dominant disorder of immune dysfunction characterized by onset of moderate to severe atopic dermatitis in early childhood. Some patients may have recurrent infections and other variable immune abnormalities. Laboratory studies show defects in T-cell activation, increased IgE, and eosinophilia. {ECO:0000269|PubMed:28628108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the costimulatory signal essential for T- cell receptor (TCR)-mediated T-cell activation. Its binding to DPP4 induces T-cell proliferation and NF-kappa-B activation in a T-cell receptor/CD3-dependent manner. Activates NF-kappa-B via BCL10 and IKK. Stimulates the phosphorylation of BCL10. Also activates the TORC1 signaling pathway. {ECO:0000269|PubMed:11278692, ECO:0000269|PubMed:11356195, ECO:0000269|PubMed:12356734, ECO:0000269|PubMed:28628108}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Ala382Thr","c.1144G>A","MODERATE","382/1154",9,{"$nulls":5},"5","263","318","189","220","256","304","0","0","0","0.0691",{"$nulls":20},"4.286768","1.27","2.715","1","-3.68","0.995","0.005","0.935",{"$nulls":3},"Unknown",-1,"AD/AR","Congenital B cell lymphocytosis; Immunodeficiency 11","Allergy/Immunology/Infectious; Oncologic","COSMIC",null,null,"C4551967| C3554686| C4539957","0/0","262,0","0","262","0/1","288,26","0.0828","314",null,"chr7:2937234:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0727"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CARD11","chr7:2937234","CARD11(A382T)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: B-cell expansion with NFKB and T-cell anergy (BENTA) [MIM:616452]: An autosomal dominant condition characterized by onset in infancy of splenomegaly and polyclonal expansion of B cells, resulting in peripheral lymphocytosis. Affected individuals also show mild immune dysfunction, including some defective antibody responses and T-cell anergy. There may be a predisposition to the development of B-cell malignancy. {ECO:0000269|PubMed:23129749, ECO:0000269|PubMed:28628108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Immunodeficiency 11 A (IMD11A) [MIM:615206]: An autosomal recessive primary immunodeficiency characterized by normal numbers of T and B-lymphocytes, but defective intracellular signaling. There is a block in B-cell differentiation with increased numbers of transitional B-cells and hypogammaglobulinemia, as well as decreased numbers of regulatory T-cells and defects in T-cell function. {ECO:0000269|PubMed:23374270, ECO:0000269|PubMed:23561803}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Immunodeficiency 11B with atopic dermatitis (IMD11B) [MIM:617638]: An autosomal dominant disorder of immune dysfunction characterized by onset of moderate to severe atopic dermatitis in early childhood. Some patients may have recurrent infections and other variable immune abnormalities. Laboratory studies show defects in T-cell activation, increased IgE, and eosinophilia. {ECO:0000269|PubMed:28628108}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the costimulatory signal essential for T- cell receptor (TCR)-mediated T-cell activation. Its binding to DPP4 induces T-cell proliferation and NF-kappa-B activation in a T-cell receptor/CD3-dependent manner. Activates NF-kappa-B via BCL10 and IKK. Stimulates the phosphorylation of BCL10. Also activates the TORC1 signaling pathway. {ECO:0000269|PubMed:11278692, ECO:0000269|PubMed:11356195, ECO:0000269|PubMed:12356734, ECO:0000269|PubMed:28628108}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Ala382Thr","c.1144G>A","MODERATE","382/1154",9,{"$nulls":5},"5","263","241","189","165","257","224","0","0","0","0.0625",{"$nulls":20},"4.286768","1.27","2.715","1","-3.68","0.995","0.005","0.935",{"$nulls":3},"Unknown",-1,"AD/AR","Congenital B cell lymphocytosis; Immunodeficiency 11","Allergy/Immunology/Infectious; Oncologic","COSMIC",null,null,"C4551967| C3554686| C4539957","0/0","262,0","0","262","0/1","221,15","0.0636","236",null,"chr7:2937234:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0545"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CASZ1","chr1:10653678","CASZ1(S793Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator (PubMed:23639441, PubMed:27693370). Involved in vascular assembly and morphogenesis through direct transcriptional regulation of EGFL7 (PubMed:23639441). {ECO:0000269|PubMed:23639441, ECO:0000269|PubMed:27693370}.; ",{"$nulls":4},"p.Ser793Tyr","c.2378_2379delCGinsAT","MODERATE","793/1759",11,{"$nulls":5},"4","328","198","282","163","267","159","0","0","0","0.0881",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","324,0","0","324","0/1","177,15","0.0781","192",null,"chr1:10653678:CG:AT",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0798"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","CELSR2","chr1:109262904","CELSR2(N1548T)",null,null,"topological domain (Extracellular ), domain (Laminin G-like 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor that may have an important role in cell/cell signaling during nervous system formation.; ",{"$nulls":4},"p.Asn1548Thr","c.4643A>C","MODERATE","1548/2923",7,{"$nulls":5},"3","828","704","579","473",null,null,"0.006","0.006",{"$nulls":22},"3.997734","-1.34","3.02","0.997659","-3.44","0.927","0.003","0.66",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","798,3","0.0037","801","0/1","616,46","0.0695","662",null,"chr1:109262904:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0677"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CELSR2","chr1:109262904","CELSR2(N1548T)",null,null,"topological domain (Extracellular ), domain (Laminin G-like 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor that may have an important role in cell/cell signaling during nervous system formation.; ",{"$nulls":4},"p.Asn1548Thr","c.4643A>C","MODERATE","1548/2923",7,{"$nulls":5},"4","828","592","579","402","744","527","0.006","0.006","0","0.0816",{"$nulls":20},"3.997734","-1.34","3.02","0.997659","-3.44","0.927","0.003","0.66",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","793,4","0.005","797","0/1","494,47","0.0869","541",null,"chr1:109262904:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0821"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","CEP89","chr19:32915451","CEP89(A484G)",null,null,"coiled-coil region , splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Homozygous deletion comprising CEP89 and SLC7A9 genes has been reported in a patient with isolated complex IV deficiency, intellectual disability and multisystemic problems that include cystinuria, cataract, broad based walking pattern and deafness. {ECO:0000269|PubMed:23575228}.; ","FUNCTION: Required for ciliogenesis. Also plays a role in mitochondrial metabolism where it may modulate complex IV activity. {ECO:0000269|PubMed:23348840, ECO:0000269|PubMed:23575228}.; ",{"$nulls":4},"p.Ala484Gly","c.1451C>G","MODERATE","484/783",14,{"$nulls":5},"4","552","512","365","325","479","439","0","0","0","0.1207",{"$nulls":20},"-0.63841","-2.32","1.15","1","-1.95","0.102","0.336","0.207",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","533,0","0","533","0/1","427,63","0.1286","490",null,"chr19:32915451:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1262"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CEP89","chr19:32915451","CEP89(A484G)",null,null,"coiled-coil region , splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=Homozygous deletion comprising CEP89 and SLC7A9 genes has been reported in a patient with isolated complex IV deficiency, intellectual disability and multisystemic problems that include cystinuria, cataract, broad based walking pattern and deafness. {ECO:0000269|PubMed:23575228}.; ","FUNCTION: Required for ciliogenesis. Also plays a role in mitochondrial metabolism where it may modulate complex IV activity. {ECO:0000269|PubMed:23348840, ECO:0000269|PubMed:23575228}.; ",{"$nulls":4},"p.Ala484Gly","c.1451C>G","MODERATE","484/783",14,{"$nulls":5},"4","552","407","365","264","476","344","0","0","0","0.1831",{"$nulls":20},"-0.63841","-2.32","1.15","1","-1.95","0.102","0.336","0.207",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","533,0","0","533","0/1","328,70","0.1759","398",null,"chr19:32915451:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.178"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CLGN","chr4:140412951","CLGN(S43I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Functions during spermatogenesis as a chaperone for a range of client proteins that are important for sperm adhesion onto the egg zona pellucida and for subsequent penetration of the zona pellucida. Required for normal sperm migration from the uterus into the oviduct. Required for normal male fertility. Binds calcium ions (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ser43Ile","c.128G>T","MODERATE","43/610",2,{"$nulls":5},"3",null,null,"74","39",{"$nulls":26},"-0.007594","0.67;0.67;-0.71","0.895;0.895;.","1","-2.07;-2.07;-2.3","0.0;0.0;.","0.167;0.167;0.161","0.098;0.084;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","82,0","0","83","0/1","42,5","0.1064","47",null,"chr4:140412951:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1282"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","COG8","chr16:69335141","COG8(D265H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Congenital disorder of glycosylation 2H (CDG2H) [MIM:611182]: CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. They are characterized by under-glycosylated serum proteins. These multisystem disorders present with a wide variety of clinical features, such as disorders of the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:17331980}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for normal Golgi function. {ECO:0000250}.; ",{"$nulls":4},"p.Asp265His","c.793G>C","MODERATE","265/612",3,{"$nulls":5},"4","460","352","378","283","388","289","0","0","0","0.0588",{"$nulls":20},"2.177972",".;.;0.79;.",".;2.72;.;.","0.999982",".;.;-3.71;-4.26","0.074;0.074;.;.",".;.;0.029;0.062",".;.;0.392;.",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type IIh","Biochemical; Hematologic; Neurologic",{"$nulls":3},"C1970021","0/0","458,0","0","458","0/1","323,23","0.0665","346",null,"chr16:69335141:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0636"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","COG8","chr16:69335141","COG8(D265H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Congenital disorder of glycosylation 2H (CDG2H) [MIM:611182]: CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation. They are characterized by under-glycosylated serum proteins. These multisystem disorders present with a wide variety of clinical features, such as disorders of the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:17331980}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for normal Golgi function. {ECO:0000250}.; ",{"$nulls":4},"p.Asp265His","c.793G>C","MODERATE","265/612",3,{"$nulls":5},"4","460","327","378","264","387","285","0","0","0","0.1053",{"$nulls":20},"2.177972",".;.;0.79;.",".;2.72;.;.","0.999982",".;.;-3.71;-4.26","0.074;0.074;.;.",".;.;0.029;0.062",".;.;0.392;.",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type IIh","Biochemical; Hematologic; Neurologic",{"$nulls":3},"C1970021","0/0","458,0","0","458","0/1","291,31","0.0963","322",null,"chr16:69335141:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0985"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","COPB2","chr3:139367065","COPB2(R542S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Microcephaly 19, primary, autosomal recessive (MCPH19) [MIM:617800]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. MCPH19 affected individuals manifest severe developmental delay, failure to thrive, cortical blindness, and spasticity. Brain imaging show a simplified gyral pattern, thin corpus callosum, slight ventricular dilation, and delayed myelination. {ECO:0000269|PubMed:29036432}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg542Ser","c.1626A>C","MODERATE","542/906",14,{"$nulls":5},"5","292","247","204","178","254","210","0","0","0","0.1667",{"$nulls":20},"3.8052099999999998","-0.3;-2.54","3.66;.","1","-5.81;-5.74","0.979;.","0.0","0.884;0.839",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The Golgi coatomer complex (see MIM 601924) constitutes the coat of nonclathrin-coated vesicles and is essential for Golgi budding and vesicular trafficking. It consists of 7 protein subunits, including COPB2.[supplied by OMIM, Jul 2002].",null,"C4540488","0/0","291,0","0","291","0/1","203,39","0.1612","242",null,"chr3:139367065:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1629"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","COPB2","chr3:139367065","COPB2(R542S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Microcephaly 19, primary, autosomal recessive (MCPH19) [MIM:617800]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. MCPH19 affected individuals manifest severe developmental delay, failure to thrive, cortical blindness, and spasticity. Brain imaging show a simplified gyral pattern, thin corpus callosum, slight ventricular dilation, and delayed myelination. {ECO:0000269|PubMed:29036432}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; ","FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg542Ser","c.1626A>C","MODERATE","542/906",14,{"$nulls":5},"5","292","240","204","173","254","199","0","0","0","0.1709",{"$nulls":20},"3.8052099999999998","-0.3;-2.54","3.66;.","1","-5.81;-5.74","0.979;.","0.0","0.884;0.839",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The Golgi coatomer complex (see MIM 601924) constitutes the coat of nonclathrin-coated vesicles and is essential for Golgi budding and vesicular trafficking. It consists of 7 protein subunits, including COPB2.[supplied by OMIM, Jul 2002].",null,"C4540488","0/0","287,0","0","287","0/1","184,42","0.1858","226",null,"chr3:139367065:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1561"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","COPS6","chr7:100091680","COPS6(G293fs)",null,null,"region of interest (Interaction with Vpr )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, c-jun/JUN, IkappaBalpha/NFKBIA, ITPK1 and IRF8, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively. Has some glucocorticoid receptor- responsive activity. Stabilizes COP1 through reducing COP1 auto- ubiquitination and decelerating COP1 turnover rate, hence regulates the ubiquitination of COP1 targets. {ECO:0000269|PubMed:11285227, ECO:0000269|PubMed:11337588, ECO:0000269|PubMed:12628923, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:21625211, ECO:0000269|PubMed:9535219}.; ",{"$nulls":4},"p.Gly293fs","c.876_877delCG","HIGH","292/327",10,{"$nulls":5},"3",null,null,"664","470",{"$nulls":11},"(COPS6|ENSG00000168090|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","927,0","0","927","0/1","649,37","0.0539","686",null,"chr7:100091680:TCG:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0574"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","CPEB1","chr15:82557988","CPEB1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Sequence-specific RNA-binding protein that regulates mRNA cytoplasmic polyadenylation and translation initiation during oocyte maturation, early development and at postsynapse sites of neurons. Binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU- 3') within the mRNA 3'-UTR. RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). In absence of phosphorylation and in association with TACC3 is also involved as a repressor of translation of CPE-containing mRNA; a repression that is relieved by phosphorylation or degradation (By similarity). Involved in the transport of CPE-containing mRNA to dendrites; those mRNAs may be transported to dendrites in a translationally dormant form and translationally activated at synapses (By similarity). Its interaction with APLP1 promotes local CPE-containing mRNA polyadenylation and translation activation (By similarity). Induces the assembly of stress granules in the absence of stress. Required for cell cycle progression, specifically for prophase entry (PubMed:26398195). {ECO:0000250|UniProtKB:P70166, ECO:0000269|PubMed:15731006, ECO:0000269|PubMed:15966895, ECO:0000269|PubMed:24990967, ECO:0000269|PubMed:26398195}.; ",{"$nulls":5},"c.560-2A>T","HIGH",null,3,{"$nulls":5},"5","326","229","235","181","305","221","0","0","0","0.1674",{"$nulls":5},"(CPEB1|ENSG00000214575|1|1.00),(AC245033.1|ENSG00000260836|1|1.00)",{"$nulls":14},"5.761163",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","325,0","0","325","0/1","189,38","0.1674","227",null,"chr15:82557988:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1768"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CPEB1","chr15:82557988","CPEB1(Splicing Acceptor/Donor Loss)",{"$nulls":6},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Sequence-specific RNA-binding protein that regulates mRNA cytoplasmic polyadenylation and translation initiation during oocyte maturation, early development and at postsynapse sites of neurons. Binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU- 3') within the mRNA 3'-UTR. RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). In absence of phosphorylation and in association with TACC3 is also involved as a repressor of translation of CPE-containing mRNA; a repression that is relieved by phosphorylation or degradation (By similarity). Involved in the transport of CPE-containing mRNA to dendrites; those mRNAs may be transported to dendrites in a translationally dormant form and translationally activated at synapses (By similarity). Its interaction with APLP1 promotes local CPE-containing mRNA polyadenylation and translation activation (By similarity). Induces the assembly of stress granules in the absence of stress. Required for cell cycle progression, specifically for prophase entry (PubMed:26398195). {ECO:0000250|UniProtKB:P70166, ECO:0000269|PubMed:15731006, ECO:0000269|PubMed:15966895, ECO:0000269|PubMed:24990967, ECO:0000269|PubMed:26398195}.; ",{"$nulls":5},"c.560-2A>T","HIGH",null,3,{"$nulls":5},"5","326","206","235","144","305","197","0","0","0","0.1523",{"$nulls":5},"(CPEB1|ENSG00000214575|1|1.00),(AC245033.1|ENSG00000260836|1|1.00)",{"$nulls":14},"5.761163",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":7},"0/0","325,0","0","325","0/1","170,30","0.15","200",null,"chr15:82557988:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1319"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CR1","chr1:207611992","CR1(P2176S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Mediates cellular binding of particles and immune complexes that have activated complement.; ",{"$nulls":4},"p.Pro2176Ser","c.6526C>T","MODERATE","2176/2489",39,{"$nulls":5},"5","924","662","747","534","781","546","0","0","0","0.0696",{"$nulls":20},"1.32896","-0.04",null,"1","-1.73;-1.73;-1.73;-1.71;-1.3",".;.;.;.;0.489","0.531;0.531;0.531;0.531;0.124","0.386;0.324;0.33;0.331;0.382",{"$nulls":3},"Unknown",-1,"BG","Blood group, Knops system","Hematologic",{"$nulls":3},"C1292327| C1970028","0/0","895,0","0","895","0/1","592,36","0.0573","628",null,"chr1:207611992:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0543"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","CXCR3","chrX:71617063","CXCR3(A184T)",null,null,"transmembrane region (Helical; Name=4 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform 1: Receptor for the C-X-C chemokine CXCL9, CXCL10 and CXCL11 and mediates the proliferation, survival and angiogenic activity of human mesangial cells (HMC) through a heterotrimeric G-protein signaling pathway (PubMed:12782716). Binds to CCL21. Probably promotes cell chemotaxis response. {ECO:0000269|PubMed:12782716}.; FUNCTION: Isoform 3: Mediates the activity of CXCL11.; ",{"$nulls":4},"p.Ala184Thr","c.550G>A","MODERATE","184/415",2,{"$nulls":5},"4","1043","747","873","626","823","600","0.001","0.001","0","0.1717",{"$nulls":20},"2.315214","-0.99",".;0.965","1","-1.09;-1.1","0.769;0.995","0.007;0.036","0.414;0.415",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1009,1","0.001","1010","0/1","599,118","0.1646","717",null,"chrX:71617063:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1581"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","CXCR3","chrX:71617063","CXCR3(A184T)",null,null,"transmembrane region (Helical; Name=4 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform 1: Receptor for the C-X-C chemokine CXCL9, CXCL10 and CXCL11 and mediates the proliferation, survival and angiogenic activity of human mesangial cells (HMC) through a heterotrimeric G-protein signaling pathway (PubMed:12782716). Binds to CCL21. Probably promotes cell chemotaxis response. {ECO:0000269|PubMed:12782716}.; FUNCTION: Isoform 3: Mediates the activity of CXCL11.; ",{"$nulls":4},"p.Ala184Thr","c.550G>A","MODERATE","184/415",2,{"$nulls":5},"4","1043","748","873","592","827","607","0.001","0.001","0","0.1993",{"$nulls":20},"2.315214","-0.99",".;0.965","1","-1.09;-1.1","0.769;0.995","0.007;0.036","0.414;0.415",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1026,1","0.001","1027","0/1","583,142","0.1959","725",null,"chrX:71617063:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1909"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","DIP2B","chr12:50714502","DIP2B(Q919H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln919His","c.2757A>T","MODERATE","919/1576",23,{"$nulls":5},"4","596","493","400","331","522","411","0","0","0","0.1314",{"$nulls":20},"2.177384","2.76","2.85","0.999948","-3.3","0.031","0.014","0.557",{"$nulls":3},"Unknown",-1,"AD","Mental retardation, FRA12A type","Neurologic",{"$nulls":3},"C1969893","0/0","586,0","0","586","0/1","403,69","0.1462","472",null,"chr12:50714502:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.148"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","DIP2B","chr12:50714502","DIP2B(Q919H)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln919His","c.2757A>T","MODERATE","919/1576",23,{"$nulls":5},"4","596","449","400","307","521","386","0","0","0","0.2021",{"$nulls":20},"2.177384","2.76","2.85","0.999948","-3.3","0.031","0.014","0.557",{"$nulls":3},"Unknown",-1,"AD","Mental retardation, FRA12A type","Neurologic",{"$nulls":3},"C1969893","0/0","585,0","0","585","0/1","342,90","0.2083","432",null,"chr12:50714502:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1922"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","DLGAP2","chr8:1668439","DLGAP2(A641T)",{"$nulls":6},255,"PASS","Missense","rs368663387",2.44140625E-4,null,"FUNCTION: May play a role in the molecular organization of synapses and neuronal cell signaling. Could be an adapter protein linking ion channel to the subsynaptic cytoskeleton. May induce enrichment of PSD-95/SAP90 at the plasma membrane.; ",{"$nulls":4},"p.Ala641Thr","c.1921G>A","MODERATE","641/1055",9,1,{"$nulls":4},"3","1027","738",{"$nulls":4},"0.001","0.001",{"$nulls":22},"3.319104",null,".;1.9;.","0.999995",null,".;1.0;.",null,".;.;0.694",{"$nulls":3},"ESP6500_AA_AF",2.44140625E-4,{"$nulls":7},"0/0","986,1","0.001","987","0/1","639,63","0.0897","702",null,"chr8:1668439:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","DLGAP2","chr8:1668439","DLGAP2(A641T)",{"$nulls":6},255,"PASS","Missense","rs368663387",2.44140625E-4,null,"FUNCTION: May play a role in the molecular organization of synapses and neuronal cell signaling. Could be an adapter protein linking ion channel to the subsynaptic cytoskeleton. May induce enrichment of PSD-95/SAP90 at the plasma membrane.; ",{"$nulls":4},"p.Ala641Thr","c.1921G>A","MODERATE","641/1055",9,1,{"$nulls":4},"3","1027","585",{"$nulls":4},"0.001","0.001",{"$nulls":22},"3.319104",null,".;1.9;.","0.999995",null,".;1.0;.",null,".;.;0.694",{"$nulls":3},"ESP6500_AA_AF",2.44140625E-4,{"$nulls":7},"0/0","1006,1","0.001","1007","0/1","528,48","0.0833","576",null,"chr8:1668439:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","DNAH5","chr5:13708186","DNAH5(S4425R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Ciliary dyskinesia, primary, 3 (CILD3) [MIM:608644]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:11062149, ECO:0000269|PubMed:11788826, ECO:0000269|PubMed:16627867, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Required for structural and functional integrity of the cilia of ependymal cells lining the brain ventricles.; ",{"$nulls":4},"p.Ser4425Arg","c.13275C>A","MODERATE","4425/4624",76,1,{"$nulls":4},"4","504","414","417","348","405","328","0","0","0","0.1677",{"$nulls":20},"0.589121","2.91","4.585","0.999999","-4.47","0.969","0.001","0.547",{"$nulls":3},"Unknown",-1,"AR","Ciliary dyskinesia, primary, 3, with or without situs inversus","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary",{"$nulls":3},"C1837618","0/0","495,0","0","495","0/1","339,65","0.1609","404",null,"chr5:13708186:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1552"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","DNAH5","chr5:13708186","DNAH5(S4425R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Ciliary dyskinesia, primary, 3 (CILD3) [MIM:608644]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269|PubMed:11062149, ECO:0000269|PubMed:11788826, ECO:0000269|PubMed:16627867, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. Required for structural and functional integrity of the cilia of ependymal cells lining the brain ventricles.; ",{"$nulls":4},"p.Ser4425Arg","c.13275C>A","MODERATE","4425/4624",76,1,{"$nulls":4},"3","504","326","417","269",null,null,"0","0",{"$nulls":22},"0.589121","2.91","4.585","0.999999","-4.47","0.969","0.001","0.547",{"$nulls":3},"Unknown",-1,"AR","Ciliary dyskinesia, primary, 3, with or without situs inversus","Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary",{"$nulls":3},"C1837618","0/0","497,0","0","497","0/1","245,75","0.2344","320",null,"chr5:13708186:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2305"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","DYNC2H1","chr11:103109654","DYNC2H1(W28_N35del)",null,null,"region of interest (Stem )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,"DISEASE: Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3) [MIM:613091]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:19361615, ECO:0000269|PubMed:19442771, ECO:0000269|PubMed:22499340, ECO:0000269|PubMed:23456818}. Note=The disease is caused by mutations affecting the gene represented in this entry. In some cases DYNC2H1 mutations result in disease phenotype in the presence of mutations in NEK1 indicating digenic inheritance (digenic short rib-polydactyly syndrome 3/6 with polydactyly) (PubMed:21211617). {ECO:0000269|PubMed:21211617}.; ","FUNCTION: May function as a motor for intraflagellar retrograde transport. Functions in cilia biogenesis. May play a role in transport between endoplasmic reticulum and Golgi or organization of the Golgi in cells (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Trp28_Asn35del","c.84_107delGGATCAGCCACTGTTGTGCAACTG","MODERATE","28/4314",1,{"$nulls":5},"4","673","323","483","227","551","267","0","0","0","0.0861",{"$nulls":31},"Unknown",-1,"AR/Digenic ","Short-rib thoracic dysplasia 3 with or without polydactyly","Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal",{"$nulls":3},"C0036069","0/0","736,0","0","736","0/1","309,25","0.0749","334",null,"chr11:103109654:TCTGGGATCAGCCACTGTTGTGCAA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0881"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","E4F1","chr16:2234715","E4F1(K576Q)",null,null,"zinc finger region (C2H2-type 9; degenerate ), region of interest (Interaction with BMI1 ), region of interest (Mediates interaction with TP53 ), region of interest (Mediates interaction with RASSF1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as a transcriptional repressor. May also function as a ubiquitin ligase mediating ubiquitination of chromatin-associated TP53. Functions in cell survival and proliferation through control of the cell cycle. Functions in the p53 and pRB tumor suppressor pathways and regulates the cyclin CCNA2 transcription.; ",{"$nulls":4},"p.Lys576Gln","c.1726A>C","MODERATE","576/784",11,{"$nulls":5},"5","1105","1082","778","747","1002","950","0","0","0","0.0989",{"$nulls":20},"3.772083","2.19","0.57;.;.","0.999995;0.993054;0.999995","-1.83;-1.69;-2.2","0.973;.;.","0.09;0.068;0.076","0.606;0.611;0.589",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1081,0","0","1081","0/1","908,114","0.1115","1022",null,"chr16:2234715:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0924"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","E4F1","chr16:2234715","E4F1(K576Q)",null,null,"zinc finger region (C2H2-type 9; degenerate ), region of interest (Interaction with BMI1 ), region of interest (Mediates interaction with TP53 ), region of interest (Mediates interaction with RASSF1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as a transcriptional repressor. May also function as a ubiquitin ligase mediating ubiquitination of chromatin-associated TP53. Functions in cell survival and proliferation through control of the cell cycle. Functions in the p53 and pRB tumor suppressor pathways and regulates the cyclin CCNA2 transcription.; ",{"$nulls":4},"p.Lys576Gln","c.1726A>C","MODERATE","576/784",11,{"$nulls":5},"5","1105","901","778","614","1001","809","0","0","0","0.1508",{"$nulls":20},"3.772083","2.19","0.57;.;.","0.999995;0.993054;0.999995","-1.83;-1.69;-2.2","0.973;.;.","0.09;0.068;0.076","0.606;0.611;0.589",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1084,0","0","1084","0/1","731,143","0.1636","874",null,"chr16:2234715:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1612"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","EOGT","chr3:69005210","EOGT(R149G)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Adams-Oliver syndrome 4 (AOS4) [MIM:615297]: A form of Adams-Oliver syndrome, a disorder characterized by the congenital absence of skin (aplasia cutis congenita) in combination with transverse limb defects. Aplasia cutis congenita can be located anywhere on the body, but in the vast majority of the cases, it is present on the posterior parietal region where it is often associated with an underlying defect of the parietal bones. Limb abnormalities are typically limb truncation defects affecting the distal phalanges or entire digits (true ectrodactyly). Only rarely, metatarsals/metacarpals or more proximal limb structures are also affected. Apart from transverse limb defects, syndactyly, most commonly of second and third toes, can also be observed. The clinical features are highly variable and can also include cardiovascular malformations, brain abnormalities and vascular defects such as cutis marmorata and dilated scalp veins. {ECO:0000269|PubMed:23522784}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalyzes the transfer of a single N-acetylglucosamine from UDP-GlcNAc to a serine or threonine residue in extracellular proteins resulting in their modification with a beta-linked N- acetylglucosamine (O-GlcNAc). Specifically glycosylates the Thr residue located between the fifth and sixth conserved cysteines of folded EGF-like domains. {ECO:0000269|PubMed:23671640}.; ",{"$nulls":4},"p.Arg149Gly","c.445C>G","MODERATE","149/527",7,{"$nulls":5},"5","222","163","156","105","193","136","0","0","0","0.0882",{"$nulls":20},"3.093214",null,"2.24","0.970108;0.503298;0.970108;1","-2.46;-2.87;.;.","0.577;0.872;0.577;0.872","0.064;0.095;.;.","0.414;0.408;0.414;0.408",{"$nulls":3},"Unknown",-1,"AR","Adams-Oliver syndrome 4","Cardiovascular; Musculoskeletal",{"$nulls":3},"C3809092","0/0","218,0","0","218","0/1","144,16","0.1","160",null,"chr3:69005210:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0857"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ERRFI1","chr1:8013330","ERRFI1(I423M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Negative regulator of EGFR signaling in skin morphogenesis. Acts as a negative regulator for several EGFR family members, including ERBB2, ERBB3 and ERBB4. Inhibits EGFR catalytic activity by interfering with its dimerization. Inhibits autophosphorylation of EGFR, ERBB2 and ERBB4. Important for normal keratinocyte proliferation and differentiation. Plays a role in modulating the response to steroid hormones in the uterus. Required for normal response to progesterone in the uterus and for fertility. Mediates epithelial estrogen responses in the uterus by regulating ESR1 levels and activation. Important for regulation of endometrium cell proliferation. Important for normal prenatal and perinatal lung development (By similarity). {ECO:0000250}.; ",null,"[ \"Afatinib\" , \"Cetuximab\" , \"Erlotinib\" , \"Gefitinib\" , \"Lapatinib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Trastuzumab\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Erlotinib\" , \"Gefitinib\" , \"Lapatinib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Trastuzumab\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Erlotinib\" , \"Gefitinib\" , \"Lapatinib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Trastuzumab\"]","p.Ile423Met","c.1269C>G","MODERATE","423/462",4,{"$nulls":5},"5","536","427","419","307","480","380","0","0","0","0.2316",{"$nulls":20},"1.191939","2.52","0.92","0.999834;0.999994","-0.39","0.022","0.174","0.058",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","526,0","0","526","0/1","308,98","0.2414","406",null,"chr1:8013330:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2345"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ERRFI1","chr1:8013330","ERRFI1(I423M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Negative regulator of EGFR signaling in skin morphogenesis. Acts as a negative regulator for several EGFR family members, including ERBB2, ERBB3 and ERBB4. Inhibits EGFR catalytic activity by interfering with its dimerization. Inhibits autophosphorylation of EGFR, ERBB2 and ERBB4. Important for normal keratinocyte proliferation and differentiation. Plays a role in modulating the response to steroid hormones in the uterus. Required for normal response to progesterone in the uterus and for fertility. Mediates epithelial estrogen responses in the uterus by regulating ESR1 levels and activation. Important for regulation of endometrium cell proliferation. Important for normal prenatal and perinatal lung development (By similarity). {ECO:0000250}.; ",null,"[ \"Afatinib\" , \"Cetuximab\" , \"Erlotinib\" , \"Gefitinib\" , \"Lapatinib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Trastuzumab\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Erlotinib\" , \"Gefitinib\" , \"Lapatinib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Trastuzumab\"]","[ \"Afatinib\" , \"Cetuximab\" , \"Erlotinib\" , \"Gefitinib\" , \"Lapatinib\" , \"Panitumumab\" , \"Pertuzumab\" , \"Trastuzumab\"]","p.Ile423Met","c.1269C>G","MODERATE","423/462",4,{"$nulls":5},"5","536","393","419","306","482","347","0","0","0","0.2939",{"$nulls":20},"1.191939","2.52","0.92","0.999834;0.999994","-0.39","0.022","0.174","0.058",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","524,0","0","524","0/1","263,110","0.2949","373",null,"chr1:8013330:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3137"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","EXD1","chr15:41196007","EXD1(D189Y)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity (By similarity). The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing- triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease (By similarity). {ECO:0000250|UniProtKB:H9IUR0, ECO:0000250|UniProtKB:Q8CDF7}.; ",{"$nulls":4},"p.Asp189Tyr","c.565G>T","MODERATE","189/572",8,{"$nulls":5},"4","190","133","138","94","163","112","0","0","0","0.0893",{"$nulls":20},"4.098618","-0.34","3.45;.","0.999983","-8.94","1.0;.","0.0","0.949;0.959",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","186,0","0","186","0/1","117,10","0.0787","127",null,"chr15:41196007:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0745"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","EXD1","chr15:41196007","EXD1(D189Y)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: RNA-binding component of the PET complex, a multiprotein complex required for the processing of piRNAs during spermatogenesis. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposable elements, preventing their mobilization, which is essential for the germline integrity (By similarity). The PET complex is required during the secondary piRNAs metabolic process for the PIWIL2 slicing- triggered loading of PIWIL4 piRNAs. In the PET complex, EXD1 probably acts as an RNA adapter. EXD1 is an inactive exonuclease (By similarity). {ECO:0000250|UniProtKB:H9IUR0, ECO:0000250|UniProtKB:Q8CDF7}.; ",{"$nulls":4},"p.Asp189Tyr","c.565G>T","MODERATE","189/572",8,{"$nulls":5},"4","190","148","138","100","162","125","0","0","0","0.072",{"$nulls":20},"4.098618","-0.34","3.45;.","0.999983","-8.94","1.0;.","0.0","0.949;0.959",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","188,0","0","188","0/1","134,11","0.0759","145",null,"chr15:41196007:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.06"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FAP","chr2:162194748","FAP(G468D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell surface glycoprotein serine protease that participates in extracellular matrix degradation and involved in many cellular processes including tissue remodeling, fibrosis, wound healing, inflammation and tumor growth. Both plasma membrane and soluble forms exhibit post-proline cleaving endopeptidase activity, with a marked preference for Ala/Ser-Gly-Pro-Ser/Asn/Ala consensus sequences, on substrate such as alpha-2-antiplasmin SERPINF2 and SPRY2 (PubMed:14751930, PubMed:16223769, PubMed:16480718, PubMed:16410248, PubMed:17381073, PubMed:18095711, PubMed:21288888, PubMed:24371721). Degrade also gelatin, heat-denatured type I collagen, but not native collagen type I and IV, vibronectin, tenascin, laminin, fibronectin, fibrin or casein (PubMed:9065413, PubMed:2172980, PubMed:7923219, PubMed:10347120, PubMed:10455171, PubMed:12376466, PubMed:16223769, PubMed:16651416, PubMed:18095711). Have also dipeptidyl peptidase activity, exhibiting the ability to hydrolyze the prolyl bond two residues from the N-terminus of synthetic dipeptide substrates provided that the penultimate residue is proline, with a preference for Ala-Pro, Ile-Pro, Gly-Pro, Arg-Pro and Pro-Pro (PubMed:10347120, PubMed:10593948, PubMed:16175601, PubMed:16223769, PubMed:16651416, PubMed:16410248, PubMed:17381073, PubMed:21314817, PubMed:24371721, PubMed:24717288). Natural neuropeptide hormones for dipeptidyl peptidase are the neuropeptide Y (NPY), peptide YY (PYY), substance P (TAC1) and brain natriuretic peptide 32 (NPPB) (PubMed:21314817). The plasma membrane form, in association with either DPP4, PLAUR or integrins, is involved in the pericellular proteolysis of the extracellular matrix (ECM), and hence promotes cell adhesion, migration and invasion through the ECM. Plays a role in tissue remodeling during development and wound healing. Participates in the cell invasiveness towards the ECM in malignant melanoma cancers. Enhances tumor growth progression by increasing angiogenesis, collagen fiber degradation and apoptosis and by reducing antitumor response of the immune system. Promotes glioma cell invasion through the brain parenchyma by degrading the proteoglycan brevican. Acts as a tumor suppressor in melanocytic cells through regulation of cell proliferation and survival in a serine protease activity-independent manner. {ECO:0000250|UniProtKB:P97321, ECO:0000269|PubMed:10347120, ECO:0000269|PubMed:10455171, ECO:0000269|PubMed:10593948, ECO:0000269|PubMed:12376466, ECO:0000269|PubMed:14751930, ECO:0000269|PubMed:16175601, ECO:0000269|PubMed:16223769, ECO:0000269|PubMed:16410248, ECO:0000269|PubMed:16480718, ECO:0000269|PubMed:16651416, ECO:0000269|PubMed:17105646, ECO:0000269|PubMed:17381073, ECO:0000269|PubMed:18095711, ECO:0000269|PubMed:20707604, ECO:0000269|PubMed:21288888, ECO:0000269|PubMed:21314817, ECO:0000269|PubMed:2172980, ECO:0000269|PubMed:24371721, ECO:0000269|PubMed:24717288, ECO:0000269|PubMed:7923219, ECO:0000269|PubMed:9065413}.; ",{"$nulls":4},"p.Gly468Asp","c.1403G>A","MODERATE","468/760",17,{"$nulls":5},"4","356","279","239","193","335","263","0","0","0","0.1027",{"$nulls":20},"4.292778",".;-3.97;1.53",".;3.475;.","1",".;-6.11;-6.16",".;1.0;0.994",".;0.0;0.0","0.922;0.942;0.932",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a homodimeric integral membrane gelatinase belonging to the serine protease family. It is selectively expressed in reactive stromal fibroblasts of epithelial cancers, granulation tissue of healing wounds, and malignant cells of bone and soft tissue sarcomas. This protein is thought to be involved in the control of fibroblast growth or epithelial-mesenchymal interactions during development, tissue repair, and epithelial carcinogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014].",null,null,"0/0","350,0","0","350","0/1","247,26","0.0952","273",null,"chr2:162194748:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1036"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FAP","chr2:162194748","FAP(G468D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cell surface glycoprotein serine protease that participates in extracellular matrix degradation and involved in many cellular processes including tissue remodeling, fibrosis, wound healing, inflammation and tumor growth. Both plasma membrane and soluble forms exhibit post-proline cleaving endopeptidase activity, with a marked preference for Ala/Ser-Gly-Pro-Ser/Asn/Ala consensus sequences, on substrate such as alpha-2-antiplasmin SERPINF2 and SPRY2 (PubMed:14751930, PubMed:16223769, PubMed:16480718, PubMed:16410248, PubMed:17381073, PubMed:18095711, PubMed:21288888, PubMed:24371721). Degrade also gelatin, heat-denatured type I collagen, but not native collagen type I and IV, vibronectin, tenascin, laminin, fibronectin, fibrin or casein (PubMed:9065413, PubMed:2172980, PubMed:7923219, PubMed:10347120, PubMed:10455171, PubMed:12376466, PubMed:16223769, PubMed:16651416, PubMed:18095711). Have also dipeptidyl peptidase activity, exhibiting the ability to hydrolyze the prolyl bond two residues from the N-terminus of synthetic dipeptide substrates provided that the penultimate residue is proline, with a preference for Ala-Pro, Ile-Pro, Gly-Pro, Arg-Pro and Pro-Pro (PubMed:10347120, PubMed:10593948, PubMed:16175601, PubMed:16223769, PubMed:16651416, PubMed:16410248, PubMed:17381073, PubMed:21314817, PubMed:24371721, PubMed:24717288). Natural neuropeptide hormones for dipeptidyl peptidase are the neuropeptide Y (NPY), peptide YY (PYY), substance P (TAC1) and brain natriuretic peptide 32 (NPPB) (PubMed:21314817). The plasma membrane form, in association with either DPP4, PLAUR or integrins, is involved in the pericellular proteolysis of the extracellular matrix (ECM), and hence promotes cell adhesion, migration and invasion through the ECM. Plays a role in tissue remodeling during development and wound healing. Participates in the cell invasiveness towards the ECM in malignant melanoma cancers. Enhances tumor growth progression by increasing angiogenesis, collagen fiber degradation and apoptosis and by reducing antitumor response of the immune system. Promotes glioma cell invasion through the brain parenchyma by degrading the proteoglycan brevican. Acts as a tumor suppressor in melanocytic cells through regulation of cell proliferation and survival in a serine protease activity-independent manner. {ECO:0000250|UniProtKB:P97321, ECO:0000269|PubMed:10347120, ECO:0000269|PubMed:10455171, ECO:0000269|PubMed:10593948, ECO:0000269|PubMed:12376466, ECO:0000269|PubMed:14751930, ECO:0000269|PubMed:16175601, ECO:0000269|PubMed:16223769, ECO:0000269|PubMed:16410248, ECO:0000269|PubMed:16480718, ECO:0000269|PubMed:16651416, ECO:0000269|PubMed:17105646, ECO:0000269|PubMed:17381073, ECO:0000269|PubMed:18095711, ECO:0000269|PubMed:20707604, ECO:0000269|PubMed:21288888, ECO:0000269|PubMed:21314817, ECO:0000269|PubMed:2172980, ECO:0000269|PubMed:24371721, ECO:0000269|PubMed:24717288, ECO:0000269|PubMed:7923219, ECO:0000269|PubMed:9065413}.; ",{"$nulls":4},"p.Gly468Asp","c.1403G>A","MODERATE","468/760",17,{"$nulls":5},"4","356","311","239","205","335","283","0","0","0","0.1413",{"$nulls":20},"4.292778",".;-3.97;1.53",".;3.475;.","1",".;-6.11;-6.16",".;1.0;0.994",".;0.0;0.0","0.922;0.942;0.932",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a homodimeric integral membrane gelatinase belonging to the serine protease family. It is selectively expressed in reactive stromal fibroblasts of epithelial cancers, granulation tissue of healing wounds, and malignant cells of bone and soft tissue sarcomas. This protein is thought to be involved in the control of fibroblast growth or epithelial-mesenchymal interactions during development, tissue repair, and epithelial carcinogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014].",null,null,"0/0","343,0","0","343","0/1","252,44","0.1486","296",null,"chr2:162194748:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1317"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FASLG","chr1:172665821","FASLG(K217K)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Autoimmune lymphoproliferative syndrome 1B (ALPS1B) [MIM:601859]: A disorder of apoptosis that manifests in early childhood and results in the accumulation of autoreactive lymphocytes. It is characterized by non-malignant lymphadenopathy with hepatosplenomegaly, and autoimmune hemolytic anemia, thrombocytopenia and neutropenia. {ECO:0000269|PubMed:26334989, ECO:0000269|PubMed:8787672}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cytokine that binds to TNFRSF6/FAS, a receptor that transduces the apoptotic signal into cells (PubMed:26334989, PubMed:9228058). Involved in cytotoxic T-cell-mediated apoptosis, natural killer cell-mediated apoptosis and in T-cell development (PubMed:9228058, PubMed:7528780, PubMed:9427603). Initiates fratricidal/suicidal activation-induced cell death (AICD) in antigen-activated T-cells contributing to the termination of immune responses (By similarity). TNFRSF6/FAS-mediated apoptosis has also a role in the induction of peripheral tolerance (By similarity). Binds to TNFRSF6B/DcR3, a decoy receptor that blocks apoptosis (PubMed:27806260). {ECO:0000250|UniProtKB:P41047, ECO:0000269|PubMed:17557115, ECO:0000269|PubMed:27806260, ECO:0000269|PubMed:7528780, ECO:0000269|PubMed:9228058, ECO:0000269|PubMed:9427603}.; FUNCTION: FasL intracellular domain: Cytoplasmic form induces gene transcription inhibition. {ECO:0000269|PubMed:17557115}.; ","level2",{"$nulls":4},"c.651G>A","HIGH",null,4,{"$nulls":5},"5","453","376","350","300","402","313","0","0","0","0.1725",{"$nulls":31},"Unknown",-1,"AD","Autoimmune lymphoproliferative syndrome, type IB","Allergy/Immunology/Infectious; Hematologic; Oncologic; Renal","kAPOPTOSIS,kCANCER,kMAPK",null,null,"C0684249| C1866120| C1328840","0/0","450,0","0","450","0/1","312,56","0.1522","368",null,"chr1:172665821:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FASLG","chr1:172665821","FASLG(K217K)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Autoimmune lymphoproliferative syndrome 1B (ALPS1B) [MIM:601859]: A disorder of apoptosis that manifests in early childhood and results in the accumulation of autoreactive lymphocytes. It is characterized by non-malignant lymphadenopathy with hepatosplenomegaly, and autoimmune hemolytic anemia, thrombocytopenia and neutropenia. {ECO:0000269|PubMed:26334989, ECO:0000269|PubMed:8787672}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cytokine that binds to TNFRSF6/FAS, a receptor that transduces the apoptotic signal into cells (PubMed:26334989, PubMed:9228058). Involved in cytotoxic T-cell-mediated apoptosis, natural killer cell-mediated apoptosis and in T-cell development (PubMed:9228058, PubMed:7528780, PubMed:9427603). Initiates fratricidal/suicidal activation-induced cell death (AICD) in antigen-activated T-cells contributing to the termination of immune responses (By similarity). TNFRSF6/FAS-mediated apoptosis has also a role in the induction of peripheral tolerance (By similarity). Binds to TNFRSF6B/DcR3, a decoy receptor that blocks apoptosis (PubMed:27806260). {ECO:0000250|UniProtKB:P41047, ECO:0000269|PubMed:17557115, ECO:0000269|PubMed:27806260, ECO:0000269|PubMed:7528780, ECO:0000269|PubMed:9228058, ECO:0000269|PubMed:9427603}.; FUNCTION: FasL intracellular domain: Cytoplasmic form induces gene transcription inhibition. {ECO:0000269|PubMed:17557115}.; ","level2",{"$nulls":4},"c.651G>A","HIGH",null,4,{"$nulls":5},"5","453","359","350","270","403","294","0","0","0","0.1735",{"$nulls":31},"Unknown",-1,"AD","Autoimmune lymphoproliferative syndrome, type IB","Allergy/Immunology/Infectious; Hematologic; Oncologic; Renal","kAPOPTOSIS,kCANCER,kMAPK",null,null,"C0684249| C1866120| C1328840","0/0","452,0","0","452","0/1","287,63","0.18","350",null,"chr1:172665821:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1926"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FBXW4","chr10:101612364","FBXW4(R317H)",null,null,"repeat (WD 4 )",{"$nulls":3},255,"PASS","Missense","rs1336995911",-1,null,"FUNCTION: Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. Likely to be involved in key signaling pathways crucial for normal limb development. May participate in Wnt signaling.; ",{"$nulls":4},"p.Arg317His","c.950G>A","MODERATE","317/412",7,{"$nulls":5},"4","265","212","214","171","200","163","0","0","0","0.1411",{"$nulls":20},"4.159183","1.89","3.295","0.999997","-4.06","1.0",null,"0.947",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","258,0","0","258","0/1","174,30","0.1471","204",null,"chr10:101612364:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.152"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FBXW4","chr10:101612364","FBXW4(R317H)",null,null,"repeat (WD 4 )",{"$nulls":3},255,"PASS","Missense","rs1336995911",-1,null,"FUNCTION: Probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. Likely to be involved in key signaling pathways crucial for normal limb development. May participate in Wnt signaling.; ",{"$nulls":4},"p.Arg317His","c.950G>A","MODERATE","317/412",7,{"$nulls":5},"4","265","167","214","145","200","134","0","0","0","0.1343",{"$nulls":20},"4.159183","1.89","3.295","0.999997","-4.06","1.0",null,"0.947",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","258,0","0","258","0/1","145,19","0.1159","164",null,"chr10:101612364:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1172"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FCGRT","chr19:49526099","FCGRT(V360M)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs200786838",8.705e-05,null,"FUNCTION: Binds to the Fc region of monomeric immunoglobulins gamma (PubMed:7964511, PubMed:10933786). Mediates the selective uptake of IgG from milk and helps newborn animals to acquire passive immunity. IgG in the milk is bound at the apical surface of the intestinal epithelium. The resultant FcRn-IgG complexes are transcytosed across the intestinal epithelium and IgG is released from FcRn into blood or tissue fluids (By similarity). Possible role in transfer of immunoglobulin G from mother to fetus (PubMed:7964511). {ECO:0000250|UniProtKB:P13599, ECO:0000269|PubMed:10933786, ECO:0000269|PubMed:7964511}.; ",{"$nulls":4},"p.Val360Met","c.1078G>A","MODERATE","360/365",7,{"$nulls":5},"5","667","578","444","369","595","510","0","0","0","0.0529",{"$nulls":20},"0.500076","5.69;5.69;.;5.8;5.5","0;0;.;.;.","1","-0.2;-0.2;.;.;.","0.42;0.42;.;.;.","0.008;0.008;.;.;.","0.088;0.088;0.109;0.085;.",{"$nulls":3},"ExAC_AMR_AF",8.705e-05,{"$nulls":7},"0/0","651,0","0","651","0/1","522,34","0.0612","556",null,"chr19:49526099:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0569"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FCGRT","chr19:49526099","FCGRT(V360M)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs200786838",8.705e-05,null,"FUNCTION: Binds to the Fc region of monomeric immunoglobulins gamma (PubMed:7964511, PubMed:10933786). Mediates the selective uptake of IgG from milk and helps newborn animals to acquire passive immunity. IgG in the milk is bound at the apical surface of the intestinal epithelium. The resultant FcRn-IgG complexes are transcytosed across the intestinal epithelium and IgG is released from FcRn into blood or tissue fluids (By similarity). Possible role in transfer of immunoglobulin G from mother to fetus (PubMed:7964511). {ECO:0000250|UniProtKB:P13599, ECO:0000269|PubMed:10933786, ECO:0000269|PubMed:7964511}.; ",{"$nulls":4},"p.Val360Met","c.1078G>A","MODERATE","360/365",7,{"$nulls":5},"5","667","527","444","345","597","461","0","0","0","0.0933",{"$nulls":20},"0.500076","5.69;5.69;.;5.8;5.5","0;0;.;.;.","1","-0.2;-0.2;.;.;.","0.42;0.42;.;.;.","0.008;0.008;.;.;.","0.088;0.088;0.109;0.085;.",{"$nulls":3},"ExAC_AMR_AF",8.705e-05,{"$nulls":7},"0/0","655,0","0","655","0/1","451,53","0.1052","504",null,"chr19:49526099:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1014"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FER1L6","chr8:124091434","FER1L6(N1468S)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs550920633",1.0224948875255625E-3,{"$nulls":6},"p.Asn1468Ser","c.4403A>G","MODERATE","1468/1857",34,{"$nulls":5},"4","164","139",null,null,"129","91","0","0","0","0.0549",{"$nulls":20},"3.938312","0.14","2.66","0.999999","-4.72","1.0",null,"0.758",{"$nulls":3},"1000Gp3_SAS_AF",1.0224948875255625E-3,{"$nulls":7},"0/0","164,0","0","164","0/1","128,7","0.0519","135",null,"chr8:124091434:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FER1L6","chr8:124091434","FER1L6(N1468S)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs550920633",1.0224948875255625E-3,{"$nulls":6},"p.Asn1468Ser","c.4403A>G","MODERATE","1468/1857",34,{"$nulls":5},"4","164","141",null,null,"128","112","0","0","0","0.1339",{"$nulls":20},"3.938312","0.14","2.66","0.999999","-4.72","1.0",null,"0.758",{"$nulls":3},"1000Gp3_SAS_AF",1.0224948875255625E-3,{"$nulls":7},"0/0","163,0","0","163","0/1","122,19","0.1348","141",null,"chr8:124091434:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FGF17","chr8:22048183","FGF17(E196fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Hypogonadotropic hypogonadism 20 with or without anosmia (HH20) [MIM:615270]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:23643382}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. Some patients carrying mutations in FGF17 also have a mutation in another HH-associated gene including FGFR1, HS6ST1 and FLRT3 (PubMed:23643382). {ECO:0000269|PubMed:23643382}.; ","FUNCTION: Plays an important role in the regulation of embryonic development and as signaling molecule in the induction and patterning of the embryonic brain. Required for normal brain development. {ECO:0000269|PubMed:16597617}.; ","level2",{"$nulls":3},"p.Glu196fs","c.586dupG","HIGH","196/216",5,{"$nulls":5},"3",null,null,"583","412","712","514",null,null,"0","0.0584",{"$nulls":5},"(FGF17|ENSG00000158815|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/Multigenic","Hypogonadotropic hypogonadism 20, with or without anosmia","Craniofacial; Endocrine; Musculoskeletal; Neurologic","kCANCER,kMAPK",null,null,"C0342384| C3808983","0/0","766,1","0.0013","767","0/1","509,30","0.0557","539",null,"chr8:22048183:C:CG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0558"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FGF17","chr8:22048183","FGF17(E196fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Hypogonadotropic hypogonadism 20 with or without anosmia (HH20) [MIM:615270]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:23643382}. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. Some patients carrying mutations in FGF17 also have a mutation in another HH-associated gene including FGFR1, HS6ST1 and FLRT3 (PubMed:23643382). {ECO:0000269|PubMed:23643382}.; ","FUNCTION: Plays an important role in the regulation of embryonic development and as signaling molecule in the induction and patterning of the embryonic brain. Required for normal brain development. {ECO:0000269|PubMed:16597617}.; ","level2",{"$nulls":3},"p.Glu196fs","c.586dupG","HIGH","196/216",5,{"$nulls":5},"4","830","495","583","332","712","418","0.0013","0.0013","0","0.0957",{"$nulls":5},"(FGF17|ENSG00000158815|1|1.00)",{"$nulls":25},"Unknown",-1,"AD/Multigenic","Hypogonadotropic hypogonadism 20, with or without anosmia","Craniofacial; Endocrine; Musculoskeletal; Neurologic","kCANCER,kMAPK",null,null,"C0342384| C3808983","0/0","767,1","0.0013","768","0/1","392,56","0.125","448",null,"chr8:22048183:C:CG",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1175"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FOXJ3","chr1:42189380","FOXJ3(T459I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator of MEF2C involved in the regulation pf adult muscle fiber type identity and skeletal muscle regeneration. {ECO:0000250|UniProtKB:Q8BUR3}.; ",{"$nulls":4},"p.Thr459Ile","c.1376C>T","MODERATE","459/622",10,{"$nulls":5},"5","371","274","255","175","339","253","0","0","0","0.0711",{"$nulls":20},"3.288597","-3.23;-3.23;-3.23;-3.25;-3.23","0.895;0.895;0.895;.;0.895","0.997687;0.997687;0.997687;0.997687;0.997687;1","-1.67;-1.67;-1.67;-1.66;-1.67","0.94;0.94;0.94;.;0.94","0.002","0.324;0.323;0.347;0.447;0.326",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","361,1","0.0028","362","0/1","245,23","0.0858","268",null,"chr1:42189380:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.08"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FOXJ3","chr1:42189380","FOXJ3(T459I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator of MEF2C involved in the regulation pf adult muscle fiber type identity and skeletal muscle regeneration. {ECO:0000250|UniProtKB:Q8BUR3}.; ",{"$nulls":4},"p.Thr459Ile","c.1376C>T","MODERATE","459/622",10,{"$nulls":5},"5","371","240","255","162","338","219","0","0","0","0.0959",{"$nulls":20},"3.288597","-3.23;-3.23;-3.23;-3.25;-3.23","0.895;0.895;0.895;.;0.895","0.997687;0.997687;0.997687;0.997687;0.997687;1","-1.67;-1.67;-1.67;-1.66;-1.67","0.94;0.94;0.94;.;0.94","0.002","0.324;0.323;0.347;0.447;0.326",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","361,1","0.0028","362","0/1","215,23","0.0966","238",null,"chr1:42189380:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0926"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FOXK1","chr7:4761069","FOXK1(E568Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional regulator that binds to the upstream enhancer region (CCAC box) of myoglobin gene (By similarity). Important regulatory factor of the myogenic progenitor cell population (By similarity). Involved in the cell cycle process, promotes proliferation by repressing Foxo4 transcriptional activity and the cyclin-dependent kinase inhibitor, p21CIP, in the myogenic progenitor cells (By similarity). Represses myogenic differentiation by inhibiting MEFC acitivity (By similarity). Has a role in remodeling processes of adult muscles that occur in response to physiological stimuli (By similarity). Required to correct temporal orchestration of molecular and cellular events necessary for muscle repair (By similarity). Positively regulates Wnt/beta-catenin signaling by translocating DVL into the nucleus (PubMed:25805136). Reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression (PubMed:25852164). {ECO:0000250|UniProtKB:P42128, ECO:0000269|PubMed:25805136, ECO:0000269|PubMed:25852164}.; ",{"$nulls":4},"p.Glu568Gln","c.1702G>C","MODERATE","568/733",8,{"$nulls":5},"5","282","246","274","240","218","191","0","0","0","0.0838",{"$nulls":20},"3.390908","-4.03","1.995","0.998199","-1.58","0.998","0.004","0.31",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","278,0","0","278","0/1","230,16","0.065","246",null,"chr7:4761069:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FOXK1","chr7:4761069","FOXK1(E568Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional regulator that binds to the upstream enhancer region (CCAC box) of myoglobin gene (By similarity). Important regulatory factor of the myogenic progenitor cell population (By similarity). Involved in the cell cycle process, promotes proliferation by repressing Foxo4 transcriptional activity and the cyclin-dependent kinase inhibitor, p21CIP, in the myogenic progenitor cells (By similarity). Represses myogenic differentiation by inhibiting MEFC acitivity (By similarity). Has a role in remodeling processes of adult muscles that occur in response to physiological stimuli (By similarity). Required to correct temporal orchestration of molecular and cellular events necessary for muscle repair (By similarity). Positively regulates Wnt/beta-catenin signaling by translocating DVL into the nucleus (PubMed:25805136). Reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression (PubMed:25852164). {ECO:0000250|UniProtKB:P42128, ECO:0000269|PubMed:25805136, ECO:0000269|PubMed:25852164}.; ",{"$nulls":4},"p.Glu568Gln","c.1702G>C","MODERATE","568/733",8,{"$nulls":5},"5","282","237","274","225","218","170","0","0","0","0.0882",{"$nulls":20},"3.390908","-4.03","1.995","0.998199","-1.58","0.998","0.004","0.31",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","279,0","0","279","0/1","220,16","0.0678","236",null,"chr7:4761069:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0667"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","FSD1L","chr9:105534522","FSD1L(S352Y)",null,null,"domain (B30.2/SPRY ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser352Tyr","c.1055C>A","MODERATE","352/530",11,1,{"$nulls":4},"4","384","425","287","309","312","344","0.0026","0.0026","0","0.0669",{"$nulls":20},"3.909699",".;1.96;1.96;2.51;1.96",".;2.11;.;.;.","0.999925;0.999925;0.999925;0.999925;0.999625;0.999925",".;-1.31;-1.4;-1.25;-1.13",".;0.998;.;0.994;.",".;0.017;0.002;0.002;0.01","0.342;0.403;0.402;0.36;0.323",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","363,1","0.0027","364","0/1","365,25","0.0641","390",null,"chr9:105534522:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0615"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","FSD1L","chr9:105534522","FSD1L(S352Y)",null,null,"domain (B30.2/SPRY ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser352Tyr","c.1055C>A","MODERATE","352/530",11,1,{"$nulls":4},"4","384","341","287","244","314","280","0.0026","0.0026","0","0.1107",{"$nulls":20},"3.909699",".;1.96;1.96;2.51;1.96",".;2.11;.;.;.","0.999925;0.999925;0.999925;0.999925;0.999625;0.999925",".;-1.31;-1.4;-1.25;-1.13",".;0.998;.;0.994;.",".;0.017;0.002;0.002;0.01","0.342;0.403;0.402;0.36;0.323",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","366,0","0","366","0/1","288,34","0.1056","322",null,"chr9:105534522:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1025"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","GAB3","chrX:154712367","GAB3(R311C)",{"$nulls":6},255,"PASS","Missense","rs782468082",1.507E-4,{"$nulls":6},"p.Arg311Cys","c.931C>T","MODERATE","311/587",4,{"$nulls":5},"5","657","480","503","370","590","410","0","0","0","0.0829",{"$nulls":20},"4.07923","1.38","3.33;.;.","0.99963","-6.01;-6.39;-6.01","1.0;.;.","0.001;0.002;0.001","0.485;0.505;0.455",{"$nulls":3},"ExAC_EAS_AF",1.507E-4,{"$nulls":7},"0/0","636,0","0","636","0/1","423,40","0.0864","463",null,"chrX:154712367:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0973"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GAB3","chrX:154712367","GAB3(R311C)",{"$nulls":6},255,"PASS","Missense","rs782468082",1.507E-4,{"$nulls":6},"p.Arg311Cys","c.931C>T","MODERATE","311/587",4,{"$nulls":5},"5","657","403","503","314","590","347","0","0","0","0.0807",{"$nulls":20},"4.07923","1.38","3.33;.;.","0.99963","-6.01;-6.39;-6.01","1.0;.;.","0.001;0.002;0.001","0.485;0.505;0.455",{"$nulls":3},"ExAC_EAS_AF",1.507E-4,{"$nulls":7},"0/0","636,0","0","636","0/1","354,33","0.0853","387",null,"chrX:154712367:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0892"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GABRR1","chr6:89180426","GABRR1(V338I)",{"$nulls":6},255,"PASS","Missense","rs192148367",1.440922190201729E-3,null,"FUNCTION: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel. Rho-1 GABA receptor could play a role in retinal neurotransmission.; ",{"$nulls":4},"p.Val338Ile","c.1012G>A","MODERATE","338/479",9,{"$nulls":5},"3",null,null,"1091","753","1244","692",null,null,"0","0.0708",{"$nulls":20},"2.56355","-2.03;-2.03;.;.;-2.03","2.025;.;.;.;.","0.999955;0.999964;0.99998","-0.11;-0.11;.;.;-0.1","1.0;1.0;.;.;.","1.0;1.0;.;.;1.0","0.522;0.564;0.531;0.531;0.5",{"$nulls":3},"1000Gp3_AMR_AF",1.440922190201729E-3,{"$nulls":7},"0/0","1423,0","0","1423","0/1","946,73","0.0716","1019",null,"chr6:89180426:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0624"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GBP6","chr1:89385420","GBP6(G618V)",{"$nulls":6},255,"PASS","Missense","rs1461098915",-1,null,"FUNCTION: Binds GTP, GDP and GMP. {ECO:0000250}.; ",{"$nulls":4},"p.Gly618Val","c.1853G>T","MODERATE","618/633",11,{"$nulls":5},"5","409","299","281","218","369","259","0","0","0","0.0849",{"$nulls":20},"-0.824779","-0.15",null,"1","-2.39",null,"0.473","0.059",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Guanylate-binding proteins, such as GBP6, are induced by interferon and hydrolyze GTP to both GDP and GMP (Olszewski et al., 2006 [PubMed 16689661]).[supplied by OMIM, Dec 2008].  ",null,null,"0/0","406,0","0","406","0/1","262,27","0.0934","289",null,"chr1:89385420:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0963"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","GGCT","chr7:30498836","GGCT(Y130*)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 4. ), splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalyzes the formation of 5-oxoproline from gamma- glutamyl dipeptides and may play a significant role in glutathione homeostasis. Induces release of cytochrome c from mitochondria with resultant induction of apoptosis. {ECO:0000269|PubMed:16765912, ECO:0000269|PubMed:18515354}.; ",{"$nulls":4},"p.Tyr130*","c.390C>G","HIGH","130/188",3,2,{"$nulls":4},"3","304","268",null,null,"266","224","0","0","0","0.0536",{"$nulls":20},"4.033103",null,null,"1;1;0.999841;0.999841;0.999841",{"$nulls":3},"0.948;0.894;0.933",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene catalyzes the formation of 5-oxoproline from gamma-glutamyl dipeptides, the penultimate step in glutathione catabolism, and may play a critical role in glutathione homeostasis. The encoded protein may also play a role in cell proliferation, and the expression of this gene is a potential marker for cancer. Pseudogenes of this gene are located on the long arm of chromosome 5 and the short arm of chromosomes 2 and 20. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010].",null,null,"0/0","297,0","0","297","0/1","236,14","0.056","250",null,"chr7:30498836:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GGCT","chr7:30498836","GGCT(Y130*)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 4. ), splice variant (In isoform 2. ), strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalyzes the formation of 5-oxoproline from gamma- glutamyl dipeptides and may play a significant role in glutathione homeostasis. Induces release of cytochrome c from mitochondria with resultant induction of apoptosis. {ECO:0000269|PubMed:16765912, ECO:0000269|PubMed:18515354}.; ",{"$nulls":4},"p.Tyr130*","c.390C>G","HIGH","130/188",3,2,{"$nulls":4},"5","304","262","230","184","268","230","0","0","0","0.0739",{"$nulls":20},"4.033103",null,null,"1;1;0.999841;0.999841;0.999841",{"$nulls":3},"0.948;0.894;0.933",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene catalyzes the formation of 5-oxoproline from gamma-glutamyl dipeptides, the penultimate step in glutathione catabolism, and may play a critical role in glutathione homeostasis. The encoded protein may also play a role in cell proliferation, and the expression of this gene is a potential marker for cancer. Pseudogenes of this gene are located on the long arm of chromosome 5 and the short arm of chromosomes 2 and 20. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2010].",null,null,"0/0","305,0","0","305","0/1","242,17","0.0656","259",null,"chr7:30498836:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0707"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","GNA13","chr17:65056394","GNA13(Q67P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems (PubMed:15240885, PubMed:16787920, PubMed:16705036, PubMed:27084452). Activates effector molecule RhoA by binding and activating RhoGEFs (ARHGEF1/p115RhoGEF, ARHGEF11/PDZ-RhoGEF and ARHGEF12/LARG) (PubMed:15240885, PubMed:12515866). GNA13-dependent Rho signaling subsequently regulates transcription factor AP-1 (activating protein-1) (By similarity). Promotes tumor cell invasion and metastasis by activating RhoA/ROCK signaling pathway (PubMed:16787920, PubMed:16705036, PubMed:27084452). Inhibits CDH1-mediated cell adhesion in process independent from Rho activation (PubMed:11976333). {ECO:0000250|UniProtKB:P27601, ECO:0000269|PubMed:11976333, ECO:0000269|PubMed:12515866, ECO:0000269|PubMed:15240885, ECO:0000269|PubMed:16705036, ECO:0000269|PubMed:16787920, ECO:0000269|PubMed:27084452}.; ","gedi|foundationOne","[ \"Bortezomib\" , \"Carfilzomib\"]","[ \"Bortezomib\" , \"Carfilzomib\"]","[ \"Bortezomib\" , \"Carfilzomib\"]","p.Gln67Pro","c.200A>C","MODERATE","67/377",1,{"$nulls":5},"5","547","454","422","336","444","356","0","0","0","0.1489",{"$nulls":20},"4.222382","-3.04","4.545","0.999999","-4.8","0.997","0.001","0.956",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","536,0","0","536","0/1","375,66","0.1497","441",null,"chr17:65056394:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1458"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GNA13","chr17:65056394","GNA13(Q67P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems (PubMed:15240885, PubMed:16787920, PubMed:16705036, PubMed:27084452). Activates effector molecule RhoA by binding and activating RhoGEFs (ARHGEF1/p115RhoGEF, ARHGEF11/PDZ-RhoGEF and ARHGEF12/LARG) (PubMed:15240885, PubMed:12515866). GNA13-dependent Rho signaling subsequently regulates transcription factor AP-1 (activating protein-1) (By similarity). Promotes tumor cell invasion and metastasis by activating RhoA/ROCK signaling pathway (PubMed:16787920, PubMed:16705036, PubMed:27084452). Inhibits CDH1-mediated cell adhesion in process independent from Rho activation (PubMed:11976333). {ECO:0000250|UniProtKB:P27601, ECO:0000269|PubMed:11976333, ECO:0000269|PubMed:12515866, ECO:0000269|PubMed:15240885, ECO:0000269|PubMed:16705036, ECO:0000269|PubMed:16787920, ECO:0000269|PubMed:27084452}.; ","gedi|foundationOne","[ \"Bortezomib\" , \"Carfilzomib\"]","[ \"Bortezomib\" , \"Carfilzomib\"]","[ \"Bortezomib\" , \"Carfilzomib\"]","p.Gln67Pro","c.200A>C","MODERATE","67/377",1,{"$nulls":5},"5","547","382","422","284","428","279","0","0","0","0.2401",{"$nulls":20},"4.222382","-3.04","4.545","0.999999","-4.8","0.997","0.001","0.956",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","532,0","0","532","0/1","286,73","0.2033","359",null,"chr17:65056394:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1972"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","GPR31","chr6:167157440","GPR31(A131V)",{"$nulls":6},255,"PASS","Missense","rs1278947218",-1,null,"FUNCTION: High-affinity receptor for 12-(S)-hydroxy-5,8,10,14- eicosatetraenoic acid (12-S-HETE). 12-(S)-HETE is an arachidonic acid metabolite secreted by platelets and tumor cells, and known to induce endothelial cells retraction allowing invasive cell access to the subendothelial matrix, which is a critical step for extravasation or metastasis. Ligand-binding lead to activation of ERK1/2 (MAPK3/MAPK1), MEK, and NF-kappa-B. {ECO:0000269|PubMed:21712392}.; ",{"$nulls":4},"p.Ala131Val","c.392C>T","MODERATE","131/319",1,{"$nulls":5},"5","333","253","284","216","273","204","0","0","0","0.1176",{"$nulls":20},"1.65117","1.04","2.515","0.985167","-3.04","0.99","0.002","0.401",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","329,0","0","329","0/1","211,37","0.1492","248",null,"chr6:167157440:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1481"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GPR31","chr6:167157440","GPR31(A131V)",{"$nulls":6},255,"PASS","Missense","rs1278947218",-1,null,"FUNCTION: High-affinity receptor for 12-(S)-hydroxy-5,8,10,14- eicosatetraenoic acid (12-S-HETE). 12-(S)-HETE is an arachidonic acid metabolite secreted by platelets and tumor cells, and known to induce endothelial cells retraction allowing invasive cell access to the subendothelial matrix, which is a critical step for extravasation or metastasis. Ligand-binding lead to activation of ERK1/2 (MAPK3/MAPK1), MEK, and NF-kappa-B. {ECO:0000269|PubMed:21712392}.; ",{"$nulls":4},"p.Ala131Val","c.392C>T","MODERATE","131/319",1,{"$nulls":5},"5","333","227","284","175","273","189","0","0","0","0.2169",{"$nulls":20},"1.65117","1.04","2.515","0.985167","-3.04","0.99","0.002","0.401",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","329,0","0","329","0/1","174,51","0.2267","225",null,"chr6:167157440:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1943"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","GSTP1","chr11:67584704","GSTP1(K55fs)",null,null,"domain (GST N-terminal ), strand ","cross-link:Glycyl_lysine_isopeptide_(Lys-Gly)_(interchain_with_G-Cter_in_ubiquitin), beta-strand:combinatorial_evidence_used_in_manual_assertion","MODERATE, LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Regulates negatively CDK5 activity via p25/p35 translocation to prevent neurodegeneration. {ECO:0000269|PubMed:21668448}.; ","level2",{"$nulls":3},"p.Lys55fs","c.164_175del<DELETE_NUC>insACCCTGTA","HIGH","55/210",4,{"$nulls":20},"67584850",{"$nulls":26},"Unknown",-1,{"$nulls":3},"dcPGX,kCANCER","Glutathione S-transferases (GSTs) are a family of enzymes that play an important role in detoxification by catalyzing the conjugation of many hydrophobic and electrophilic compounds with reduced glutathione. Based on their biochemical, immunologic, and structural properties, the soluble GSTs are categorized into 4 main classes: alpha, mu, pi, and theta. This GST family member is a polymorphic gene encoding active, functionally different GSTP1 variant proteins that are thought to function in xenobiotic metabolism and play a role in susceptibility to cancer, and other diseases. [provided by RefSeq, Jul 2008].  ",{"$nulls":11},"chr11:67584704:<DELETE_NUC>:ACCCTGTA",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","GSTP1","chr11:67584704","GSTP1(K55fs)",null,null,"domain (GST N-terminal ), strand ","cross-link:Glycyl_lysine_isopeptide_(Lys-Gly)_(interchain_with_G-Cter_in_ubiquitin), beta-strand:combinatorial_evidence_used_in_manual_assertion","MODERATE, LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Regulates negatively CDK5 activity via p25/p35 translocation to prevent neurodegeneration. {ECO:0000269|PubMed:21668448}.; ","level2",{"$nulls":3},"p.Lys55fs","c.164_175del<DELETE_NUC>insACCCTGTA","HIGH","55/210",4,{"$nulls":20},"67584850",{"$nulls":26},"Unknown",-1,{"$nulls":3},"dcPGX,kCANCER","Glutathione S-transferases (GSTs) are a family of enzymes that play an important role in detoxification by catalyzing the conjugation of many hydrophobic and electrophilic compounds with reduced glutathione. Based on their biochemical, immunologic, and structural properties, the soluble GSTs are categorized into 4 main classes: alpha, mu, pi, and theta. This GST family member is a polymorphic gene encoding active, functionally different GSTP1 variant proteins that are thought to function in xenobiotic metabolism and play a role in susceptibility to cancer, and other diseases. [provided by RefSeq, Jul 2008].  ",{"$nulls":11},"chr11:67584704:<DELETE_NUC>:ACCCTGTA",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","HEPACAM","chr11:124921211","HEPACAM(R393H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Leukoencephalopathy, megalencephalic, with subcortical cysts, 2A (MLC2A) [MIM:613925]: A neurodegenerative disorder characterized by infantile-onset macrocephaly and later onset of motor deterioration, with ataxia and spasticity, seizures, and cognitive decline of variable severity. The brain appears swollen on magnetic resonance imaging with white-matter abnormalities and subcortical cysts, in all stages of the disease. {ECO:0000269|PubMed:21419380}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leukoencephalopathy, megalencephalic, with subcortical cysts, 2B (MLC2B) [MIM:613926]: A neurodegenerative disorder characterized by infantile-onset of macrocephaly and mildly delayed motor development associated with white-matter abnormalities on brain magnetic resonance imaging. The phenotype is milder that MLC2A, with better preserved cerebellar white matter and no subcortical cysts outside the temporal region. On follow-up, patients show normal or almost normal motor function. Some patients have normal intelligence, whereas others have a significant cognitive deficiency. {ECO:0000269|PubMed:21419380}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in regulating cell motility and cell-matrix interactions. May inhibit cell growth through suppression of cell proliferation. {ECO:0000269|PubMed:15885354, ECO:0000269|PubMed:15917256}.; ",{"$nulls":4},"p.Arg393His","c.1178G>A","MODERATE","393/416",7,{"$nulls":5},"5","173","127","135","91","157","107","0","0","0","0.0748",{"$nulls":20},"3.495832","0.36","2.095","0.997645","-0.44","0.957","0.017","0.058",{"$nulls":3},"Unknown",-1,"AD/AR","Megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without mental retardation; Megalencephalic leukoencephalopathy with subcortical cysts 2A","Neurologic",{"$nulls":3},"C3151355| C1858854| CN034246| C3151356","0/0","169,0","0","169","0/1","112,10","0.082","122",null,"chr11:124921211:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0769"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","HEPACAM","chr11:124921211","HEPACAM(R393H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Leukoencephalopathy, megalencephalic, with subcortical cysts, 2A (MLC2A) [MIM:613925]: A neurodegenerative disorder characterized by infantile-onset macrocephaly and later onset of motor deterioration, with ataxia and spasticity, seizures, and cognitive decline of variable severity. The brain appears swollen on magnetic resonance imaging with white-matter abnormalities and subcortical cysts, in all stages of the disease. {ECO:0000269|PubMed:21419380}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leukoencephalopathy, megalencephalic, with subcortical cysts, 2B (MLC2B) [MIM:613926]: A neurodegenerative disorder characterized by infantile-onset of macrocephaly and mildly delayed motor development associated with white-matter abnormalities on brain magnetic resonance imaging. The phenotype is milder that MLC2A, with better preserved cerebellar white matter and no subcortical cysts outside the temporal region. On follow-up, patients show normal or almost normal motor function. Some patients have normal intelligence, whereas others have a significant cognitive deficiency. {ECO:0000269|PubMed:21419380}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in regulating cell motility and cell-matrix interactions. May inhibit cell growth through suppression of cell proliferation. {ECO:0000269|PubMed:15885354, ECO:0000269|PubMed:15917256}.; ",{"$nulls":4},"p.Arg393His","c.1178G>A","MODERATE","393/416",7,{"$nulls":5},"5","173","84","135","60","156","70","0","0","0","0.1571",{"$nulls":20},"3.495832","0.36","2.095","0.997645","-0.44","0.957","0.017","0.058",{"$nulls":3},"Unknown",-1,"AD/AR","Megalencephalic leukoencephalopathy with subcortical cysts 2B, remitting, with or without mental retardation; Megalencephalic leukoencephalopathy with subcortical cysts 2A","Neurologic",{"$nulls":3},"C3151355| C1858854| CN034246| C3151356","0/0","169,0","0","169","0/1","68,12","0.15","80",null,"chr11:124921211:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","HERC2","chr15:28169653","HERC2(V3354M)",{"$nulls":6},255,"PASS","Missense","rs748208313",4.513e-05,"DISEASE: Mental retardation, autosomal recessive 38 (MRT38) [MIM:615516]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT38 is characterized by global developmental delay affecting motor, speech, adaptive, and social development. Patients manifest autistic features, aggression, self-injury, impulsivity, and distractibility. {ECO:0000269|PubMed:23065719}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: E3 ubiquitin-protein ligase that regulates ubiquitin- dependent retention of repair proteins on damaged chromosomes. Recruited to sites of DNA damage in response to ionizing radiation (IR) and facilitates the assembly of UBE2N and RNF8 promoting DNA damage-induced formation of 'Lys-63'-linked ubiquitin chains. Acts as a mediator of binding specificity between UBE2N and RNF8. Involved in the maintenance of RNF168 levels. E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of XPA which influences the circadian oscillation of DNA excision repair activity. By controlling the steady-state expression of the IGF1R receptor, indirectly regulates the insulin-like growth factor receptor signaling pathway (PubMed:26692333). {ECO:0000269|PubMed:20023648, ECO:0000269|PubMed:20304803, ECO:0000269|PubMed:22508508, ECO:0000269|PubMed:26692333}.; ",{"$nulls":4},"p.Val3354Met","c.10060G>A","MODERATE","3354/4834",66,{"$nulls":5},"5","548","356","379","251","530","336","0","0","0","0.0625",{"$nulls":20},"2.884859","1.04","2.2","1","-1.13","0.999","0.052","0.704",{"$nulls":3},"ExAC_NFE_AF",4.513e-05,"AD/AR","Skin/hair/eye pigmentation 1; Mental retardation, autosomal recessive 38","Dermatologic; Neurologic",{"$nulls":3},"C0032897| C1856895| C3809753","0/0","528,1","0.0019","529","0/1","318,22","0.0647","340",null,"chr15:28169653:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0637"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","IARS","chr9:92210858","IARS(L1246F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the specific attachment of an amino acid to its cognate tRNA in a 2 step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. {ECO:0000269|PubMed:8052601}.; ",{"$nulls":4},"p.Leu1246Phe","c.3738G>C","MODERATE","1246/1262",34,{"$nulls":5},"5","364","293","275","209","305","242","0","0","0","0.0785",{"$nulls":20},"3.724167","2.51;2.5","2.93;.","0.999996;0.999996;0.999996;1","-1.29","0.999;.","0.0","0.542;0.55",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAS, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Isoleucine-tRNA synthetase belongs to the class-I aminoacyl-tRNA synthetase family and has been identified as a target of autoantibodies in the autoimmune disease polymyositis/dermatomyositis. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2012].",null,null,"0/0","361,0","0","361","0/1","261,23","0.081","284",null,"chr9:92210858:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0813"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","IARS","chr9:92210858","IARS(L1246F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the specific attachment of an amino acid to its cognate tRNA in a 2 step reaction: the amino acid (AA) is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. {ECO:0000269|PubMed:8052601}.; ",{"$nulls":4},"p.Leu1246Phe","c.3738G>C","MODERATE","1246/1262",34,{"$nulls":5},"5","364","333","275","250","306","276","0","0","0","0.0725",{"$nulls":20},"3.724167","2.51;2.5","2.93;.","0.999996;0.999996;0.999996;1","-1.29","0.999;.","0.0","0.542;0.55",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAS, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Isoleucine-tRNA synthetase belongs to the class-I aminoacyl-tRNA synthetase family and has been identified as a target of autoantibodies in the autoimmune disease polymyositis/dermatomyositis. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2012].",null,null,"0/0","361,0","0","361","0/1","300,25","0.0769","325",null,"chr9:92210858:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.076"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","IDS","chrX:149498295","IDS(P174T)",null,null,"disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Mucopolysaccharidosis 2 (MPS2) [MIM:309900]: An X-linked lysosomal storage disease characterized by intracellular accumulation of heparan sulfate and dermatan sulfate and their excretion in urine. Most children with MPS2 have a severe form with early somatic abnormalities including skeletal deformities, hepatosplenomegaly, and progressive cardiopulmonary deterioration. A prominent feature is neurological damage that presents as developmental delay and hyperactivity but progresses to mental retardation and dementia. They die before 15 years of age, usually as a result of obstructive airway disease or cardiac failure. In contrast, those with a mild form of MPS2 may survive into adulthood, with attenuated somatic complications and often without mental retardation. {ECO:0000269|PubMed:10215411, ECO:0000269|PubMed:10220152, ECO:0000269|PubMed:10447264, ECO:0000269|PubMed:10671065, ECO:0000269|PubMed:10838181, ECO:0000269|PubMed:11015461, ECO:0000269|PubMed:11683780, ECO:0000269|PubMed:11731225, ECO:0000269|PubMed:12655569, ECO:0000269|PubMed:12794697, ECO:0000269|PubMed:1284597, ECO:0000269|PubMed:1303211, ECO:0000269|PubMed:16699754, ECO:0000269|PubMed:7581397, ECO:0000269|PubMed:7599640, ECO:0000269|PubMed:7728156, ECO:0000269|PubMed:7866405, ECO:0000269|PubMed:7887413, ECO:0000269|PubMed:7981716, ECO:0000269|PubMed:8281149, ECO:0000269|PubMed:8566953, ECO:0000269|PubMed:8664909, ECO:0000269|PubMed:8830188, ECO:0000269|PubMed:8940265, ECO:0000269|PubMed:9222763, ECO:0000269|PubMed:9266380, ECO:0000269|PubMed:9375851, ECO:0000269|PubMed:9452044, ECO:0000269|PubMed:9501270, ECO:0000269|PubMed:9660053, ECO:0000269|PubMed:9762601, ECO:0000269|PubMed:9875019, ECO:0000269|PubMed:9921913, ECO:0000269|PubMed:9950361}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for the lysosomal degradation of heparan sulfate and dermatan sulfate.; ",{"$nulls":4},"p.Pro174Thr","c.520C>A","MODERATE","174/550",5,{"$nulls":5},"3",null,null,"133","102",{"$nulls":26},"1.4346130000000001","-4.89","1.715","0.983582;0.999997;0.999997;0.999997","-1.39","0.336;0.143","0.383;0.225","0.223;0.225",{"$nulls":3},"Unknown",-1,"XL","Mucopolysaccharidosis type II","Biochemical; Cardiovascular",{"$nulls":3},"C0026705","0/0","165,0","0","165","0/1","122,8","0.0615","130",null,"chrX:149498295:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0686"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","IDS","chrX:149498295","IDS(P174T)",null,null,"disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Mucopolysaccharidosis 2 (MPS2) [MIM:309900]: An X-linked lysosomal storage disease characterized by intracellular accumulation of heparan sulfate and dermatan sulfate and their excretion in urine. Most children with MPS2 have a severe form with early somatic abnormalities including skeletal deformities, hepatosplenomegaly, and progressive cardiopulmonary deterioration. A prominent feature is neurological damage that presents as developmental delay and hyperactivity but progresses to mental retardation and dementia. They die before 15 years of age, usually as a result of obstructive airway disease or cardiac failure. In contrast, those with a mild form of MPS2 may survive into adulthood, with attenuated somatic complications and often without mental retardation. {ECO:0000269|PubMed:10215411, ECO:0000269|PubMed:10220152, ECO:0000269|PubMed:10447264, ECO:0000269|PubMed:10671065, ECO:0000269|PubMed:10838181, ECO:0000269|PubMed:11015461, ECO:0000269|PubMed:11683780, ECO:0000269|PubMed:11731225, ECO:0000269|PubMed:12655569, ECO:0000269|PubMed:12794697, ECO:0000269|PubMed:1284597, ECO:0000269|PubMed:1303211, ECO:0000269|PubMed:16699754, ECO:0000269|PubMed:7581397, ECO:0000269|PubMed:7599640, ECO:0000269|PubMed:7728156, ECO:0000269|PubMed:7866405, ECO:0000269|PubMed:7887413, ECO:0000269|PubMed:7981716, ECO:0000269|PubMed:8281149, ECO:0000269|PubMed:8566953, ECO:0000269|PubMed:8664909, ECO:0000269|PubMed:8830188, ECO:0000269|PubMed:8940265, ECO:0000269|PubMed:9222763, ECO:0000269|PubMed:9266380, ECO:0000269|PubMed:9375851, ECO:0000269|PubMed:9452044, ECO:0000269|PubMed:9501270, ECO:0000269|PubMed:9660053, ECO:0000269|PubMed:9762601, ECO:0000269|PubMed:9875019, ECO:0000269|PubMed:9921913, ECO:0000269|PubMed:9950361}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Required for the lysosomal degradation of heparan sulfate and dermatan sulfate.; ",{"$nulls":4},"p.Pro174Thr","c.520C>A","MODERATE","174/550",5,{"$nulls":5},"3",null,null,"133","89",{"$nulls":26},"1.4346130000000001","-4.89","1.715","0.983582;0.999997;0.999997;0.999997","-1.39","0.336;0.143","0.383;0.225","0.223;0.225",{"$nulls":3},"Unknown",-1,"XL","Mucopolysaccharidosis type II","Biochemical; Cardiovascular",{"$nulls":3},"C0026705","0/0","165,0","0","165","0/1","110,10","0.0833","120",null,"chrX:149498295:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0562"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","IL16","chr15:81273150","IL16(V246I)",{"$nulls":6},255,"PASS","Missense","rs761815193",0.001037,null,"FUNCTION: Interleukin-16 stimulates a migratory response in CD4+ lymphocytes, monocytes, and eosinophils. Primes CD4+ T-cells for IL-2 and IL-15 responsiveness. Also induces T-lymphocyte expression of interleukin 2 receptor. Ligand for CD4.; FUNCTION: Isoform 3 is involved in cell cycle progression in T- cells. Appears to be involved in transcriptional regulation of SKP2 and is probably part of a transcriptional repression complex on the core promoter of the SKP2 gene. May act as a scaffold for GABPB1 (the DNA-binding subunit the GABP transcription factor complex) and HDAC3 thus maintaining transcriptional repression and blocking cell cycle progression in resting T-cells.; ",{"$nulls":4},"p.Val246Ile","c.736G>A","MODERATE","246/1332",5,{"$nulls":5},"5","467","410","330","268","418","368","0","0","0","0.0951",{"$nulls":20},"3.391057","0.94",".;0.66;0.66","0.999993","-0.97;-0.77;-0.7",".;1.0;1.0","0.048;0.059;0.059",".;0.636;0.661",{"$nulls":3},"ExAC_SAS_AF",0.001037,{"$nulls":4},"The protein encoded by this gene is a pleiotropic cytokine that functions as a chemoattractant, a modulator of T cell activation, and an inhibitor of HIV replication. The signaling process of this cytokine is mediated by CD4. The product of this gene undergoes proteolytic processing, which is found to yield two functional proteins. The cytokine function is exclusively attributed to the secreted C-terminal peptide, while the N-terminal product may play a role in cell cycle control. Caspase 3 is reported to be involved in the proteolytic processing of this protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010].",null,null,"0/0","449,0","0","449","0/1","348,45","0.1145","393",null,"chr15:81273150:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1157"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","IL16","chr15:81273150","IL16(V246I)",{"$nulls":6},255,"PASS","Missense","rs761815193",0.001037,null,"FUNCTION: Interleukin-16 stimulates a migratory response in CD4+ lymphocytes, monocytes, and eosinophils. Primes CD4+ T-cells for IL-2 and IL-15 responsiveness. Also induces T-lymphocyte expression of interleukin 2 receptor. Ligand for CD4.; FUNCTION: Isoform 3 is involved in cell cycle progression in T- cells. Appears to be involved in transcriptional regulation of SKP2 and is probably part of a transcriptional repression complex on the core promoter of the SKP2 gene. May act as a scaffold for GABPB1 (the DNA-binding subunit the GABP transcription factor complex) and HDAC3 thus maintaining transcriptional repression and blocking cell cycle progression in resting T-cells.; ",{"$nulls":4},"p.Val246Ile","c.736G>A","MODERATE","246/1332",5,{"$nulls":5},"5","467","357","330","247","417","336","0","0","0","0.1131",{"$nulls":20},"3.391057","0.94",".;0.66;0.66","0.999993","-0.97;-0.77;-0.7",".;1.0;1.0","0.048;0.059;0.059",".;0.636;0.661",{"$nulls":3},"ExAC_SAS_AF",0.001037,{"$nulls":4},"The protein encoded by this gene is a pleiotropic cytokine that functions as a chemoattractant, a modulator of T cell activation, and an inhibitor of HIV replication. The signaling process of this cytokine is mediated by CD4. The product of this gene undergoes proteolytic processing, which is found to yield two functional proteins. The cytokine function is exclusively attributed to the secreted C-terminal peptide, while the N-terminal product may play a role in cell cycle control. Caspase 3 is reported to be involved in the proteolytic processing of this protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010].",null,null,"0/0","449,0","0","449","0/1","306,40","0.1156","346",null,"chr15:81273150:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1053"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","INCA1","chr17:4988419","INCA1(A233S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to CDK2-bound cyclins and inhibits the kinase activity of CDK2; binding to cyclins is critical for its function as CDK inhibitor (PubMed:21540187). Inhibits cell growth and cell proliferation and may play a role in cell cycle control (By similarity). Required for ING5-mediated regulation of S-phase progression, enhancement of Fas-induced apoptosis and inhibition of cell growth (By similarity). {ECO:0000250|UniProtKB:Q6PKN7, ECO:0000269|PubMed:21540187}.; ",{"$nulls":4},"p.Ala233Ser","c.697G>T","MODERATE","233/236",8,{"$nulls":5},"4","686","531","554","407","575","432","0.0015","0.0015","0","0.1343",{"$nulls":20},"1.0083",null,".;.;-1.79;-1.79","0.998545","0.6;.;.;.","0.0;0.0;0.001;0.001","1.0;.;.;.","0.128;0.128;0.124;0.124",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","664,1","0.0015","665","0/1","433,73","0.1443","506",null,"chr17:4988419:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1327"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","INCA1","chr17:4988419","INCA1(A233S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to CDK2-bound cyclins and inhibits the kinase activity of CDK2; binding to cyclins is critical for its function as CDK inhibitor (PubMed:21540187). Inhibits cell growth and cell proliferation and may play a role in cell cycle control (By similarity). Required for ING5-mediated regulation of S-phase progression, enhancement of Fas-induced apoptosis and inhibition of cell growth (By similarity). {ECO:0000250|UniProtKB:Q6PKN7, ECO:0000269|PubMed:21540187}.; ",{"$nulls":4},"p.Ala233Ser","c.697G>T","MODERATE","233/236",8,{"$nulls":5},"4","686","451","554","352","575","361","0.0015","0.0015","0","0.2188",{"$nulls":20},"1.0083",null,".;.;-1.79;-1.79","0.998545","0.6;.;.;.","0.0;0.0;0.001;0.001","1.0;.;.;.","0.128;0.128;0.124;0.124",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","665,1","0.0015","666","0/1","341,98","0.2232","439",null,"chr17:4988419:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2188"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","INTS5","chr11:62653176","INTS5(P25R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.; ",{"$nulls":4},"p.Pro25Arg","c.74C>G","MODERATE","25/1019",1,{"$nulls":5},"4","422","354","284","234","396","322","0","0","0","0.0652",{"$nulls":20},"4.292159",null,"0.345","0.878846","-0.27","0.997","0.069","0.473",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","408,0","0","408","0/1","315,27","0.0789","342",null,"chr11:62653176:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0641"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","INTS5","chr11:62653176","INTS5(P25R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.; ",{"$nulls":4},"p.Pro25Arg","c.74C>G","MODERATE","25/1019",1,{"$nulls":5},"4","422","310","284","215","396","275","0","0","0","0.0691",{"$nulls":20},"4.292159",null,"0.345","0.878846","-0.27","0.997","0.069","0.473",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","408,0","0","408","0/1","278,25","0.0825","303",null,"chr11:62653176:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0977"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ITGAX","chr16:31363210","ITGAX(H516Y)",null,null,"topological domain (Extracellular ), repeat (FG-GAP 6 ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Integrin alpha-X/beta-2 is a receptor for fibrinogen. It recognizes the sequence G-P-R in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis.; ",{"$nulls":4},"p.His516Tyr","c.1546C>T","MODERATE","516/1169",14,1,{"$nulls":4},"5","432","342","367","293","353","288","0","0","0","0.0903",{"$nulls":20},"3.028767","3.92","1.88;.","0.981137","-4.72","1.0;.","0.001","0.287;0.274",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","430,1","0.0023","431","0/1","309,26","0.0776","335",null,"chr16:31363210:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0785"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","KCNH4","chr17:42160050","KCNH4(T1015M)",{"$nulls":6},255,"PASS","Missense","rs755934067",0.0004778,null,"FUNCTION: Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current, but shows no inactivation. Channel properties may be modulated by cAMP and subunit assembly.; ",{"$nulls":4},"p.Thr1015Met","c.3044C>T","MODERATE","1015/1017",16,{"$nulls":5},"5","209","145","184","128","161","109","0","0","0","0.2936",{"$nulls":20},"3.320323",".;-5.29","0.805","0.845608",".;-0.69","0.995",".;0.0","0.152;0.153",{"$nulls":3},"ExAC_EAS_AF",0.0004778,{"$nulls":7},"0/0","208,0","0","208","0/1","107,37","0.2569","144",null,"chr17:42160050:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2422"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","KCNH4","chr17:42160050","KCNH4(T1015M)",{"$nulls":6},255,"PASS","Missense","rs755934067",0.0004778,null,"FUNCTION: Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current, but shows no inactivation. Channel properties may be modulated by cAMP and subunit assembly.; ",{"$nulls":4},"p.Thr1015Met","c.3044C>T","MODERATE","1015/1017",16,{"$nulls":5},"5","209","112","184","100","161","85","0","0","0","0.4471",{"$nulls":20},"3.320323",".;-5.29","0.805","0.845608",".;-0.69","0.995",".;0.0","0.152;0.153",{"$nulls":3},"ExAC_EAS_AF",0.0004778,{"$nulls":7},"0/0","208,0","0","208","0/1","72,40","0.3571","112",null,"chr17:42160050:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.36"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","KIAA1429","chr8:94527008","KIAA1429(W400fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Trp400fs","c.1199_1235delGGGTAACAGCTTTAGAAGAAATTCCAAGTTTAATAAT","HIGH","400/1812",8,{"$nulls":5},"3",null,null,"316","320","344","328",null,null,"0","0.0823",{"$nulls":5},"(VIRMA|ENSG00000164944|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","543,0","0","543","0/1","501,31","0.0583","532",null,"chr8:94527008:TATTATTAAACTTGGAATTTCTTCTAAAGCTGTTACCC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0531"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","KIAA1429","chr8:94527008","KIAA1429(W400fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Trp400fs","c.1199_1235delGGGTAACAGCTTTAGAAGAAATTCCAAGTTTAATAAT","HIGH","400/1812",8,{"$nulls":5},"3",null,null,"316","276","344","280",null,null,"0","0.0893",{"$nulls":5},"(VIRMA|ENSG00000164944|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","544,0","0","544","0/1","434,27","0.0586","461",null,"chr8:94527008:TATTATTAAACTTGGAATTTCTTCTAAAGCTGTTACCC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0797"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","KIAA1549L","chr11:33591255","KIAA1549L(Y1232N)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Tyr1232Asn","c.3694T>A","MODERATE","1232/1849",11,{"$nulls":5},"5","296","251","260","216","224","194","0","0","0","0.1598",{"$nulls":20},"4.479985",null,".;2.645","0.99961;0.99961;1",".;-7.45",null,".;0.0",".;0.921",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","300,0","0","300","0/1","218,32","0.128","250",null,"chr11:33591255:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1157"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","KIAA1549L","chr11:33591255","KIAA1549L(Y1232N)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Tyr1232Asn","c.3694T>A","MODERATE","1232/1849",11,{"$nulls":5},"5","296","234","260","198","223","178","0","0","0","0.191",{"$nulls":20},"4.479985",null,".;2.645","0.99961;0.99961;1",".;-7.45",null,".;0.0",".;0.921",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","300,0","0","300","0/1","193,38","0.1645","231",null,"chr11:33591255:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1717"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","KIAA1755","chr20:38213322","KIAA1755(W1108L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Trp1108Leu","c.3323G>T","MODERATE","1108/1200",14,{"$nulls":5},"4","582","494","473","387","486","392","0","0","0","0.1633",{"$nulls":20},"2.885913","3.37","1.905","0.905785","-3.94","0.965","0.076","0.406",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","574,0","0","574","0/1","395,75","0.1596","470",null,"chr20:38213322:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.155"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","KIAA1755","chr20:38213322","KIAA1755(W1108L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Trp1108Leu","c.3323G>T","MODERATE","1108/1200",14,{"$nulls":5},"4","582","460","473","374","486","386","0","0","0","0.2487",{"$nulls":20},"2.885913","3.37","1.905","0.905785","-3.94","0.965","0.076","0.406",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","571,0","0","571","0/1","350,95","0.2135","445",null,"chr20:38213322:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2219"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","KIF14","chr1:200553548","KIF14(K1592_E1595del)",null,null,"region of interest (Required for CIT-binding ), sequence variant (In MCPH20; drastically decreased expression at the mRNA level; loss of localization at the midbody during cytokinesis and consequently loss of CIT/CRIK recruitment to the midbody. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,"DISEASE: Meckel syndrome 12 (MKS12) [MIM:616258]: A form of Meckel syndrome, a disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269|PubMed:24128419}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Microcephaly 20, primary, autosomal recessive (MCPH20) [MIM:617914]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. MCPH20 features include mild to moderate intellectual disability, autistic features, poor speech. Disease severity is highly variable. {ECO:0000269|PubMed:28892560, ECO:0000269|PubMed:29343805}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease-causing variant NM_014875.2:c.263T>A, which produces a premature truncation of the protein at Leu-88 (p.Leu88Ter), may also partly result in the deletion of 372 bp of exon 2 of KIF14 by activation of a cryptic splice site. This in-frame deletion predicts a protein that lacks 124 aa (p.Gly58-Leu181del). The disease-causing mutation NM_014875.2:c.3662G>T, resulting in the missence variant p.Gly1221Val, may also induce the skipping of exon 24, resulting in a protein that misses 76 aa (p.Gly1221_ Lys1296delinsVal). {ECO:0000269|PubMed:28892560}.; ","FUNCTION: Microtubule motor protein that binds to microtubules with high affinity through each tubulin heterodimer and has an ATPase activity (By similarity). Plays a role in many processes like cell division, cytokinesis and also in cell proliferation and apoptosis (PubMed:24784001, PubMed:16648480). During cytokinesis, targets to central spindle and midbody through its interaction with PRC1 and CIT respectively (PubMed:16431929). Regulates cell growth through regulation of cell cycle progression and cytokinesis (PubMed:24854087). During cell cycle progression acts through SCF-dependent proteasomal ubiquitin-dependent protein catabolic process which controls CDKN1B degradation, resulting in positive regulation of cyclins, including CCNE1, CCND1 and CCNB1 (PubMed:24854087). During late neurogenesis, regulates the cerebellar, cerebral cortex and olfactory bulb development through regulation of apoptosis, cell proliferation and cell division (By similarity). Also is required for chromosome congression and alignment during mitotic cell cycle process (PubMed:15843429). Regulates cell spreading, focal adhesion dynamics, and cell migration through its interaction with RADIL resulting in regulation of RAP1A-mediated inside-out integrin activation by tethering RADIL on microtubules (PubMed:23209302). {ECO:0000250|UniProtKB:L0N7N1, ECO:0000269|PubMed:15843429, ECO:0000269|PubMed:16431929, ECO:0000269|PubMed:16648480, ECO:0000269|PubMed:23209302, ECO:0000269|PubMed:24784001, ECO:0000269|PubMed:24854087}.; ",{"$nulls":4},"p.Lys1592_Glu1595del","c.4775_4786delAACCCTGGGAAA","MODERATE","1592/1648",30,{"$nulls":5},"4",null,null,"260","228","284","255",null,null,"0","0.0627",{"$nulls":31},"Unknown",-1,{"$nulls":4},"KIF14 is a member of the kinesin superfamily of microtubule-associated motors (see MIM 148760) that play important roles in intracellular transport and cell division (Nakagawa et al., 1997 [PubMed 9275178]).[supplied by OMIM, Mar 2008].  ",null,"C4693572| C4015701","0/0","346,0","0","346","0/1","292,21","0.0671","313",null,"chr1:200553548:GTTTCCCAGGGTT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0702"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","KIF14","chr1:200553548","KIF14(K1592_E1595del)",null,null,"region of interest (Required for CIT-binding ), sequence variant (In MCPH20; drastically decreased expression at the mRNA level; loss of localization at the midbody during cytokinesis and consequently loss of CIT/CRIK recruitment to the midbody. )",{"$nulls":3},255,"PASS","Inframe Indel",null,-1,"DISEASE: Meckel syndrome 12 (MKS12) [MIM:616258]: A form of Meckel syndrome, a disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269|PubMed:24128419}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Microcephaly 20, primary, autosomal recessive (MCPH20) [MIM:617914]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. MCPH20 features include mild to moderate intellectual disability, autistic features, poor speech. Disease severity is highly variable. {ECO:0000269|PubMed:28892560, ECO:0000269|PubMed:29343805}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease-causing variant NM_014875.2:c.263T>A, which produces a premature truncation of the protein at Leu-88 (p.Leu88Ter), may also partly result in the deletion of 372 bp of exon 2 of KIF14 by activation of a cryptic splice site. This in-frame deletion predicts a protein that lacks 124 aa (p.Gly58-Leu181del). The disease-causing mutation NM_014875.2:c.3662G>T, resulting in the missence variant p.Gly1221Val, may also induce the skipping of exon 24, resulting in a protein that misses 76 aa (p.Gly1221_ Lys1296delinsVal). {ECO:0000269|PubMed:28892560}.; ","FUNCTION: Microtubule motor protein that binds to microtubules with high affinity through each tubulin heterodimer and has an ATPase activity (By similarity). Plays a role in many processes like cell division, cytokinesis and also in cell proliferation and apoptosis (PubMed:24784001, PubMed:16648480). During cytokinesis, targets to central spindle and midbody through its interaction with PRC1 and CIT respectively (PubMed:16431929). Regulates cell growth through regulation of cell cycle progression and cytokinesis (PubMed:24854087). During cell cycle progression acts through SCF-dependent proteasomal ubiquitin-dependent protein catabolic process which controls CDKN1B degradation, resulting in positive regulation of cyclins, including CCNE1, CCND1 and CCNB1 (PubMed:24854087). During late neurogenesis, regulates the cerebellar, cerebral cortex and olfactory bulb development through regulation of apoptosis, cell proliferation and cell division (By similarity). Also is required for chromosome congression and alignment during mitotic cell cycle process (PubMed:15843429). Regulates cell spreading, focal adhesion dynamics, and cell migration through its interaction with RADIL resulting in regulation of RAP1A-mediated inside-out integrin activation by tethering RADIL on microtubules (PubMed:23209302). {ECO:0000250|UniProtKB:L0N7N1, ECO:0000269|PubMed:15843429, ECO:0000269|PubMed:16431929, ECO:0000269|PubMed:16648480, ECO:0000269|PubMed:23209302, ECO:0000269|PubMed:24784001, ECO:0000269|PubMed:24854087}.; ",{"$nulls":4},"p.Lys1592_Glu1595del","c.4775_4786delAACCCTGGGAAA","MODERATE","1592/1648",30,{"$nulls":5},"4",null,null,"260","226","284","266",null,null,"0","0.0752",{"$nulls":31},"Unknown",-1,{"$nulls":4},"KIF14 is a member of the kinesin superfamily of microtubule-associated motors (see MIM 148760) that play important roles in intracellular transport and cell division (Nakagawa et al., 1997 [PubMed 9275178]).[supplied by OMIM, Mar 2008].  ",null,"C4693572| C4015701","0/0","347,0","0","347","0/1","290,21","0.0675","311",null,"chr1:200553548:GTTTCCCAGGGTT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0796"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","KY","chr3:134620775","KY(I189T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable cytoskeleton-associated protease required for normal muscle growth. Involved in function, maturation and stabilization of the neuromuscular junction. May act by cleaving muscle-specific proteins such as FLNC (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ile189Thr","c.566T>C","MODERATE","189/661",7,{"$nulls":5},"5","591","502","432","359","513","433","0","0","0","0.0624",{"$nulls":20},"3.82999","1.56",".;3.275;.","0.999965","-4.11;-4.11;-4.05","1.0;0.999;1.0","0.002;0.002;0.001","0.944;0.945;0.965",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310711","0/0","581,0","0","581","0/1","449,32","0.0665","481",null,"chr3:134620775:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0613"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","KY","chr3:134620775","KY(I189T)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Probable cytoskeleton-associated protease required for normal muscle growth. Involved in function, maturation and stabilization of the neuromuscular junction. May act by cleaving muscle-specific proteins such as FLNC (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ile189Thr","c.566T>C","MODERATE","189/661",7,{"$nulls":5},"5","591","422","432","297","512","373","0","0","0","0.0777",{"$nulls":20},"3.82999","1.56",".;3.275;.","0.999965","-4.11;-4.11;-4.05","1.0;0.999;1.0","0.002;0.002;0.001","0.944;0.945;0.965",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310711","0/0","581,0","0","581","0/1","377,37","0.0894","414",null,"chr3:134620775:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0707"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","LCTL","chr15:66561310","LCTL(L161fs)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,null,"gedi",{"$nulls":3},"p.Leu161fs","c.481-15_485delTCTCTGTGTTCACAGCTGCT","HIGH","161/567",5,{"$nulls":5},"5","364","252","272","186","253","164","0","0","0","0.1707",{"$nulls":5},"(LCTL|ENSG00000188501|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","347,0","0","347","0/1","205,30","0.1277","235",null,"chr15:66561310:GAGCAGCTGTGAACACAGAGA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1505"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","LCTL","chr15:66561310","LCTL(L161fs)",null,null,"topological domain (Extracellular ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,null,"gedi",{"$nulls":3},"p.Leu161fs","c.481-15_485delTCTCTGTGTTCACAGCTGCT","HIGH","161/567",5,{"$nulls":5},"5","364","213","272","155","253","149","0","0","0","0.1611",{"$nulls":5},"(LCTL|ENSG00000188501|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","347,0","0","347","0/1","171,26","0.132","197",null,"chr15:66561310:GAGCAGCTGTGAACACAGAGA:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1226"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","LGALS1","chr22:37678558","LGALS1(D55E)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Lectin that binds beta-galactoside and a wide array of complex carbohydrates. Plays a role in regulating apoptosis, cell proliferation and cell differentiation. Inhibits CD45 protein phosphatase activity and therefore the dephosphorylation of Lyn kinase. Strong inducer of T-cell apoptosis. {ECO:0000269|PubMed:14617626, ECO:0000269|PubMed:18796645, ECO:0000269|PubMed:19497882, ECO:0000269|PubMed:24945728}.; ",{"$nulls":4},"p.Asp55Glu","c.165C>A","MODERATE","55/135",3,{"$nulls":5},"4","1126","968","830","681","990","846","0","0","0","0.1868",{"$nulls":20},"2.172116","0.79","2.465","0.998317","-3.35","1.0",null,"0.392",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1091,0","0","1091","0/1","760,176","0.188","936",null,"chr22:37678558:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.185"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","LGALS1","chr22:37678558","LGALS1(D55E)",{"$nulls":3},"beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Lectin that binds beta-galactoside and a wide array of complex carbohydrates. Plays a role in regulating apoptosis, cell proliferation and cell differentiation. Inhibits CD45 protein phosphatase activity and therefore the dephosphorylation of Lyn kinase. Strong inducer of T-cell apoptosis. {ECO:0000269|PubMed:14617626, ECO:0000269|PubMed:18796645, ECO:0000269|PubMed:19497882, ECO:0000269|PubMed:24945728}.; ",{"$nulls":4},"p.Asp55Glu","c.165C>A","MODERATE","55/135",3,{"$nulls":5},"4","1126","937","830","656","992","828","0","0","0","0.1908",{"$nulls":20},"2.172116","0.79","2.465","0.998317","-3.35","1.0",null,"0.392",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1086,0","0","1086","0/1","707,181","0.2038","888",null,"chr22:37678558:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1905"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","LGI4","chr19:35126492","LGI4(H359L)",null,null,"repeat (EAR 4 ), splice variant (In isoform 2. ), sequence variant (In AMCNMY. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of Schwann cell signaling pathway(s) that controls axon segregation and myelin formation (By similarity). {ECO:0000250|UniProtKB:Q8K1S1}.; ",{"$nulls":4},"p.His359Leu","c.1076_1077delACinsTA","MODERATE","359/537",8,{"$nulls":5},"4","365","295","315","248","326","251","0","0","0","0.1036",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C4479539","0/0","365,0","0","365","0/1","261,32","0.1092","293",null,"chr19:35126492:GT:TA",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1048"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","LGI4","chr19:35126492","LGI4(H359L)",null,null,"repeat (EAR 4 ), splice variant (In isoform 2. ), sequence variant (In AMCNMY. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of Schwann cell signaling pathway(s) that controls axon segregation and myelin formation (By similarity). {ECO:0000250|UniProtKB:Q8K1S1}.; ",{"$nulls":4},"p.His359Leu","c.1076_1077delACinsTA","MODERATE","359/537",8,{"$nulls":5},"4","365","218","315","179","325","190","0","0","0","0.1737",{"$nulls":31},"Unknown",-1,{"$nulls":6},"C4479539","0/0","365,0","0","365","0/1","180,36","0.1667","216",null,"chr19:35126492:GT:TA",0,0,"blockSubstitution","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1788"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","LRRTM4","chr2:77518479","LRRTM4(K465*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May play a role in the development and maintenance of the vertebrate nervous system. Exhibits strong synaptogenic activity, restricted to excitatory presynaptic differentiation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Lys465*","c.1393A>T","HIGH","465/591",2,{"$nulls":5},"4","573","469","433","342","513","420","0","0","0","0.069",{"$nulls":5},"(LRRTM4|ENSG00000176204|1|1.00)","(LRRTM4|ENSG00000176204|1|1.00)",{"$nulls":13},"7.052177",null,null,"1",{"$nulls":3},"0.416;0.39;0.42;0.428;0.421",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","558,0","0","558","0/1","419,31","0.0689","450",null,"chr2:77518479:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0702"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","LUZP4","chrX:115306602","LUZP4(A247D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Export adapter involved in mRNA nuclear export in cancer cells. Binds and enhances the RNA-binding activity of the nuclear RNA export factor NXF1. Can restore mRNA export function in cells compromised by loss of mRNA export adapters (PubMed:25662211). {ECO:0000269|PubMed:25662211}.; ",{"$nulls":4},"p.Ala247Asp","c.740C>A","MODERATE","247/313",4,{"$nulls":5},"3","660","426","492","320",null,null,"0","0",{"$nulls":22},"-0.385702","-1.18","0.695","1","-0.62","0.828","0.087","0.163",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","647,0","0","647","0/1","390,28","0.067","418",null,"chrX:115306602:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","MARCH5","chr10:92349466","MARCH5(D163N)",{"$nulls":6},255,"PASS","Missense","rs370134787",-1,null,"FUNCTION: Mitochondrial E3 ubiquitin-protein ligase that plays a crucial role in the control of mitochondrial morphology by acting as a positive regulator of mitochondrial fission. May play a role in the prevention of cell senescence acting as a regulator of mitochondrial quality control. Promotes ubiquitination of FIS1, DNM1L and MFN1. {ECO:0000269|PubMed:16874301, ECO:0000269|PubMed:17606867, ECO:0000269|PubMed:19741096, ECO:0000269|PubMed:20103533}.; ",{"$nulls":4},"p.Asp163Asn","c.487G>A","MODERATE","163/278",4,{"$nulls":5},"5","507","376","385","294","465","341","0","0","0","0.0587",{"$nulls":20},"3.057675","0.78","2.15","1","-3.91","0.35","0.042","0.585",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","499,0","0","499","0/1","349,22","0.0593","371",null,"chr10:92349466:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0612"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","MARCH5","chr10:92349466","MARCH5(D163N)",{"$nulls":6},255,"PASS","Missense","rs370134787",-1,null,"FUNCTION: Mitochondrial E3 ubiquitin-protein ligase that plays a crucial role in the control of mitochondrial morphology by acting as a positive regulator of mitochondrial fission. May play a role in the prevention of cell senescence acting as a regulator of mitochondrial quality control. Promotes ubiquitination of FIS1, DNM1L and MFN1. {ECO:0000269|PubMed:16874301, ECO:0000269|PubMed:17606867, ECO:0000269|PubMed:19741096, ECO:0000269|PubMed:20103533}.; ",{"$nulls":4},"p.Asp163Asn","c.487G>A","MODERATE","163/278",4,{"$nulls":5},"5","507","325","385","249","467","297","0","0","0","0.0943",{"$nulls":20},"3.057675","0.78","2.15","1","-3.91","0.35","0.042","0.585",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","499,0","0","499","0/1","289,32","0.0997","321",null,"chr10:92349466:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0843"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","MLLT6","chr17:38721972","MLLT6(T846S)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving MLLT6 is associated with acute leukemias. Translocation t(11;17)(q23;q21) with KMT2A/MLL1. The result is a rogue activator protein.; ",null,"level2",{"$nulls":3},"p.Thr846Ser","c.2537C>G","MODERATE","846/1093",17,{"$nulls":5},"5","111","97","82","70","97","85","0","0","0","0.0824",{"$nulls":20},"1.497022",null,"-0.255","0.540262",null,"0.001",null,"0.073",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","106,0","0","106","0/1","89,8","0.0825","97",null,"chr17:38721972:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","MLLT6","chr17:38721972","MLLT6(T846S)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving MLLT6 is associated with acute leukemias. Translocation t(11;17)(q23;q21) with KMT2A/MLL1. The result is a rogue activator protein.; ",null,"level2",{"$nulls":3},"p.Thr846Ser","c.2537C>G","MODERATE","846/1093",17,{"$nulls":5},"5","111","91","82","74","98","68","0","0","0","0.1029",{"$nulls":20},"1.497022",null,"-0.255","0.540262",null,"0.001",null,"0.073",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","101,0","0","101","0/1","73,9","0.1098","82",null,"chr17:38721972:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1216"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","MTUS2","chr13:29025703","MTUS2(H345Q)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds microtubules. Together with MAPRE1 may target the microtubule depolymerase KIF2C to the plus-end of microtubules. May regulate the dynamics of microtubules at their growing distal tip. {ECO:0000269|PubMed:19543227}.; ",{"$nulls":4},"p.His345Gln","c.1035C>G","MODERATE","345/1379",3,{"$nulls":5},"5","670","587","544","462","554","490","0","0","0","0.0714",{"$nulls":20},"-1.189361",null,null,"1",{"$nulls":3},"0.092",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","664,0","0","664","0/1","527,38","0.0673","565",null,"chr13:29025703:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0671"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","MTUS2","chr13:29025703","MTUS2(H345Q)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds microtubules. Together with MAPRE1 may target the microtubule depolymerase KIF2C to the plus-end of microtubules. May regulate the dynamics of microtubules at their growing distal tip. {ECO:0000269|PubMed:19543227}.; ",{"$nulls":4},"p.His345Gln","c.1035C>G","MODERATE","345/1379",3,{"$nulls":5},"5","670","495","544","373","553","408","0","0","0","0.0907",{"$nulls":20},"-1.189361",null,null,"1",{"$nulls":3},"0.092",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","666,0","0","666","0/1","443,44","0.0903","487",null,"chr13:29025703:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0858"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","MYBL1","chr8:66592501","MYBL1(K269M)",null,null,"region of interest (Transcriptional activation domain )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that specifically recognizes the sequence 5'-YAAC[GT]G-3' (PubMed:8058310, PubMed:7987850). Acts as a master regulator of male meiosis by promoting expression of piRNAs: activates expression of both piRNA precursor RNAs and expression of protein-coding genes involved in piRNA metabolism (By similarity). The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons, which is essential for the germline integrity (By similarity). {ECO:0000250|UniProtKB:P51960, ECO:0000269|PubMed:7987850, ECO:0000269|PubMed:8058310}.; ",{"$nulls":4},"p.Lys269Met","c.806A>T","MODERATE","269/752",8,{"$nulls":5},"5","240","174","161","117","212","152","0","0","0","0.0658",{"$nulls":20},"4.067534","2.36;1.88","2.42","1","-5.12;-5.02","1.0;.","0.0","0.6;0.526",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","235,0","0","235","0/1","156,15","0.0877","171",null,"chr8:66592501:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0684"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NAV3","chr12:78051028","NAV3(I799M)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration disrupting NAV3 has been found in patients with Sezary syndrome (PubMed:16166283). Translocation t(12;18)(q21;q21.2) (PubMed:16166283). {ECO:0000269|PubMed:16166283}.; ","FUNCTION: May regulate IL2 production by T-cells. May be involved in neuron regeneration. {ECO:0000269|PubMed:16166283}.; ",{"$nulls":4},"p.Ile799Met","c.2397T>G","MODERATE","799/2385",11,{"$nulls":5},"4","636","485","478","355","588","443","0","0","0","0.0564",{"$nulls":20},"0.714091","1.68;1.67;.","0.65;0.65;.","0.517511;0.517511;0.778689;0.990444","-0.59;-0.59;.","0.002;0.001;.","0.223;0.219;.","0.15;0.205;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","625,0","0","625","0/1","434,31","0.0667","465",null,"chr12:78051028:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0648"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NAV3","chr12:78051028","NAV3(I799M)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration disrupting NAV3 has been found in patients with Sezary syndrome (PubMed:16166283). Translocation t(12;18)(q21;q21.2) (PubMed:16166283). {ECO:0000269|PubMed:16166283}.; ","FUNCTION: May regulate IL2 production by T-cells. May be involved in neuron regeneration. {ECO:0000269|PubMed:16166283}.; ",{"$nulls":4},"p.Ile799Met","c.2397T>G","MODERATE","799/2385",11,{"$nulls":5},"4","636","373","478","282","589","343","0","0","0","0.0875",{"$nulls":20},"0.714091","1.68;1.67;.","0.65;0.65;.","0.517511;0.517511;0.778689;0.990444","-0.59;-0.59;.","0.002;0.001;.","0.223;0.219;.","0.15;0.205;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","625,0","0","625","0/1","326,29","0.0817","355",null,"chr12:78051028:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0957"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NEBL","chr10:20809820","NEBL(L866P)",null,null,"region of interest (Linker ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}.; ",{"$nulls":4},"p.Leu866Pro","c.2597T>C","MODERATE","866/1014",25,{"$nulls":5},"5","189","217","143","156","145","158","0","0","0","0.0633",{"$nulls":20},"3.2984970000000002","2.91","2.565","1","-5.73","0.548","0.001","0.889",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a nebulin like protein that is abundantly expressed in cardiac muscle. The encoded protein binds actin and interacts with thin filaments and Z-line associated proteins in striated muscle. This protein may be involved in cardiac myofibril assembly. A shorter isoform of this protein termed LIM nebulette is expressed in non-muscle cells and may function as a component of focal adhesion complexes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010].",null,null,"0/0","185,0","0","185","0/1","192,17","0.0813","209",null,"chr10:20809820:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0833"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NEBL","chr10:20809820","NEBL(L866P)",null,null,"region of interest (Linker ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}.; ",{"$nulls":4},"p.Leu866Pro","c.2597T>C","MODERATE","866/1014",25,{"$nulls":5},"5","189","271","143","189","146","212","0","0","0","0.0519",{"$nulls":20},"3.2984970000000002","2.91","2.565","1","-5.73","0.548","0.001","0.889",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a nebulin like protein that is abundantly expressed in cardiac muscle. The encoded protein binds actin and interacts with thin filaments and Z-line associated proteins in striated muscle. This protein may be involved in cardiac myofibril assembly. A shorter isoform of this protein termed LIM nebulette is expressed in non-muscle cells and may function as a component of focal adhesion complexes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010].",null,null,"0/0","185,0","0","185","0/1","245,14","0.0541","259",null,"chr10:20809820:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0529"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NEDD4L","chr18:58396214","NEDD4L(R1237Q)",{"$nulls":6},255,"PASS","Missense","rs777624478",0.0002188,"DISEASE: Periventricular nodular heterotopia 7 (PVNH7) [MIM:617201]: A form of periventricular nodular heterotopia, a disorder resulting from a defect in the pattern of neuronal migration in which ectopic collections of neurons lie along the lateral ventricles of the brain or just beneath, contiguously or in isolated patches. PVNH7 is an autosomal dominant disease characterized by delayed psychomotor development, intellectual disability, and seizures in some patients. Additional features include cleft palate and toe syndactyly. {ECO:0000269|PubMed:27694961}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Inhibits TGF-beta signaling by triggering SMAD2 and TGFBR1 ubiquitination and proteasome-dependent degradation. Promotes ubiquitination and internalization of various plasma membrane channels such as ENaC, SCN2A/Nav1.2, SCN3A/Nav1.3, SCN5A/Nav1.5, SCN9A/Nav1.7, SCN10A/Nav1.8, KCNA3/Kv1.3, KCNH2, EAAT1, KCNQ2/Kv7.2, KCNQ3/Kv7.3 or CLC5 (PubMed:26363003, PubMed:27445338). Promotes ubiquitination and degradation of SGK1 and TNK2. Ubiquitinates BRAT1 and this ubiquitination is enhanced in the presence of NDFIP1 (PubMed:25631046). Plays a role in dendrite formation by melanocytes (PubMed:23999003). Involved in the regulation of TOR signaling (PubMed:27694961). Ubiquitinates and regulates protein levels of NTRK1 once this one is activated by NGF (PubMed:27445338). {ECO:0000250|UniProtKB:Q8CFI0, ECO:0000269|PubMed:12911626, ECO:0000269|PubMed:15040001, ECO:0000269|PubMed:15217910, ECO:0000269|PubMed:15489223, ECO:0000269|PubMed:15496141, ECO:0000269|PubMed:15576372, ECO:0000269|PubMed:19144635, ECO:0000269|PubMed:23999003, ECO:0000269|PubMed:25631046, ECO:0000269|PubMed:26363003, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:27694961}.; ",{"$nulls":4},"p.Arg1237Gln","c.3710G>A","MODERATE","1237/1254",27,{"$nulls":5},"5","523","394","376","278","436","331","0","0","0","0.0634",{"$nulls":20},"3.98298","0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;.;0.32",".;2.16;.;.;.;.;.;.;.;.;.;.;.","1","-2.28;-2.38;.;-2.28;-2.19;-2.22;-2.22;-2.38;.;-2.22;-2.22;.;.","0.999;1.0;.;1.0;.;.;.;0.999;0.999;.;.;.;.","0.133;0.075;.;0.289;0.122;0.09;0.378;0.073;.;0.378;0.09;.;.","0.767;0.755;0.719;0.73;0.746;0.722;0.766;0.775;0.76;0.775;0.766;.;.",{"$nulls":3},"ExAC_AFR_AF",0.0002188,{"$nulls":6},"C4310669","0/0","507,0","0","507","0/1","332,26","0.0726","358",null,"chr18:58396214:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0719"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NEDD4L","chr18:58396214","NEDD4L(R1237Q)",{"$nulls":6},255,"PASS","Missense","rs777624478",0.0002188,"DISEASE: Periventricular nodular heterotopia 7 (PVNH7) [MIM:617201]: A form of periventricular nodular heterotopia, a disorder resulting from a defect in the pattern of neuronal migration in which ectopic collections of neurons lie along the lateral ventricles of the brain or just beneath, contiguously or in isolated patches. PVNH7 is an autosomal dominant disease characterized by delayed psychomotor development, intellectual disability, and seizures in some patients. Additional features include cleft palate and toe syndactyly. {ECO:0000269|PubMed:27694961}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Inhibits TGF-beta signaling by triggering SMAD2 and TGFBR1 ubiquitination and proteasome-dependent degradation. Promotes ubiquitination and internalization of various plasma membrane channels such as ENaC, SCN2A/Nav1.2, SCN3A/Nav1.3, SCN5A/Nav1.5, SCN9A/Nav1.7, SCN10A/Nav1.8, KCNA3/Kv1.3, KCNH2, EAAT1, KCNQ2/Kv7.2, KCNQ3/Kv7.3 or CLC5 (PubMed:26363003, PubMed:27445338). Promotes ubiquitination and degradation of SGK1 and TNK2. Ubiquitinates BRAT1 and this ubiquitination is enhanced in the presence of NDFIP1 (PubMed:25631046). Plays a role in dendrite formation by melanocytes (PubMed:23999003). Involved in the regulation of TOR signaling (PubMed:27694961). Ubiquitinates and regulates protein levels of NTRK1 once this one is activated by NGF (PubMed:27445338). {ECO:0000250|UniProtKB:Q8CFI0, ECO:0000269|PubMed:12911626, ECO:0000269|PubMed:15040001, ECO:0000269|PubMed:15217910, ECO:0000269|PubMed:15489223, ECO:0000269|PubMed:15496141, ECO:0000269|PubMed:15576372, ECO:0000269|PubMed:19144635, ECO:0000269|PubMed:23999003, ECO:0000269|PubMed:25631046, ECO:0000269|PubMed:26363003, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:27694961}.; ",{"$nulls":4},"p.Arg1237Gln","c.3710G>A","MODERATE","1237/1254",27,{"$nulls":5},"5","523","363","376","266","435","304","0","0","0","0.0724",{"$nulls":20},"3.98298","0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;0.32;.;0.32",".;2.16;.;.;.;.;.;.;.;.;.;.;.","1","-2.28;-2.38;.;-2.28;-2.19;-2.22;-2.22;-2.38;.;-2.22;-2.22;.;.","0.999;1.0;.;1.0;.;.;.;0.999;0.999;.;.;.;.","0.133;0.075;.;0.289;0.122;0.09;0.378;0.073;.;0.378;0.09;.;.","0.767;0.755;0.719;0.73;0.746;0.722;0.766;0.775;0.76;0.775;0.766;.;.",{"$nulls":3},"ExAC_AFR_AF",0.0002188,{"$nulls":6},"C4310669","0/0","507,0","0","507","0/1","308,27","0.0806","335",null,"chr18:58396214:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0714"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NHLH1","chr1:160370855","NHLH1(G42W)",{"$nulls":6},255,"PASS","Missense","rs764417015",-1,null,"FUNCTION: May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.; ",{"$nulls":4},"p.Gly42Trp","c.124G>T","MODERATE","42/133",2,1,{"$nulls":4},"5","353","277","296","222","269","220","0","0","0","0.1182",{"$nulls":20},"2.267076","-3.81","0.345","0.995037","-1.52","0.147","0.005","0.338",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The helix-loop-helix (HLH) proteins are a family of putative transcription factors, some of which have been shown to play an important role in growth and development of a wide variety of tissues and species. Four members of this family have been clearly implicated in tumorigenesis via their involvement in chromosomal translocations in lymphoid tumors: MYC (MIM 190080), LYL1 (MIM 151440), E2A (MIM 147141), and SCL (MIM 187040).[supplied by OMIM, Nov 2002].  ",null,null,"0/0","348,0","0","348","0/1","237,33","0.1222","270",null,"chr1:160370855:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1351"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NHLH1","chr1:160370855","NHLH1(G42W)",{"$nulls":6},255,"PASS","Missense","rs764417015",-1,null,"FUNCTION: May serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system.; ",{"$nulls":4},"p.Gly42Trp","c.124G>T","MODERATE","42/133",2,1,{"$nulls":4},"5","353","243","296","199","269","176","0","0","0","0.267",{"$nulls":20},"2.267076","-3.81","0.345","0.995037","-1.52","0.147","0.005","0.338",{"$nulls":3},"Unknown",-1,{"$nulls":4},"The helix-loop-helix (HLH) proteins are a family of putative transcription factors, some of which have been shown to play an important role in growth and development of a wide variety of tissues and species. Four members of this family have been clearly implicated in tumorigenesis via their involvement in chromosomal translocations in lymphoid tumors: MYC (MIM 190080), LYL1 (MIM 151440), E2A (MIM 147141), and SCL (MIM 187040).[supplied by OMIM, Nov 2002].  ",null,null,"0/0","348,0","0","348","0/1","175,57","0.2457","232",null,"chr1:160370855:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2261"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NLRP11","chr19:55801636","NLRP11(L703I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in inflammation. {ECO:0000305}.; ",{"$nulls":4},"p.Leu703Ile","c.2107C>A","MODERATE","703/1033",5,{"$nulls":5},"4","520","428","357","304","452","353","0.0019","0.0019","0","0.0595",{"$nulls":20},"-0.667737","0.64",".;.;1.74","1",null,"0.013;.;0.003",null,"0.229;0.196;0.184",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","501,1","0.002","502","0/1","382,24","0.0591","406",null,"chr19:55801636:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0691"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NLRP11","chr19:55801636","NLRP11(L703I)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in inflammation. {ECO:0000305}.; ",{"$nulls":4},"p.Leu703Ile","c.2107C>A","MODERATE","703/1033",5,{"$nulls":5},"4","520","385","357","283","451","331","0.0019","0.0019","0","0.0604",{"$nulls":20},"-0.667737","0.64",".;.;1.74","1",null,"0.013;.;0.003",null,"0.229;0.196;0.184",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","506,0","0","506","0/1","349,26","0.0693","375",null,"chr19:55801636:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0636"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NLRP5","chr19:56027389","NLRP5(P386A)",null,null,"domain (NACHT )",{"$nulls":3},255,"PASS","Missense","rs1474029776",-1,null,"FUNCTION: As a member of the subcortical maternal complex (SCMC), plays an essential role for zygotes to progress beyond the first embryonic cell divisions. {ECO:0000250}.; ","tcga-gbm",{"$nulls":3},"p.Pro386Ala","c.1156C>G","MODERATE","386/1200",7,{"$nulls":5},"4","713","481","584","379",null,null,"0","0",{"$nulls":22},"2.388856",".;-1.21",".;3.005","1",".;-7.66",".;0.999",".;0.0","0.455;0.47",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","707,0","0","707","0/1","442,24","0.0515","466",null,"chr19:56027389:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0528"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NOL9","chr1:6554239","NOL9(S88R)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Polynucleotide 5'-kinase involved in rRNA processing. The kinase activity is required for the processing of the 32S precursor into 5.8S and 28S rRNAs, more specifically for the generation of the major 5.8S(S) form. In vitro, has both DNA and RNA 5'-kinase activities. Probably binds RNA. {ECO:0000269|PubMed:21063389}.; ",{"$nulls":4},"p.Ser88Arg","c.264C>A","MODERATE","88/702",1,{"$nulls":5},"4","253","164","199","126","201","127","0","0","0","0.1024",{"$nulls":20},"1.6280299999999999","2.2",null,"1","-0.69","0.001","0.219","0.142",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","245,0","0","245","0/1","144,15","0.0943","159",null,"chr1:6554239:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1032"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NRP1","chr10:33185660","NRP1(I800T)",null,null,"topological domain (Extracellular ), domain (MAM ), splice variant (In isoform 2 and isoform 3. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: The membrane-bound isoform 1 is a receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. It mediates the chemorepulsant activity of semaphorins. It binds to semaphorin 3A, The PLGF-2 isoform of PGF, The VEGF165 isoform of VEGFA and VEGFB. Coexpression with KDR results in increased VEGF165 binding to KDR as well as increased chemotaxis. Regulate VEGF-induced angiogenesis. Binding to VEGFA initiates a signaling pathway needed for motor neuron axon guidance and cell body migration, including for the caudal migration of facial motor neurons from rhombomere 4 to rhombomere 6 during embryonic development (By similarity). {ECO:0000250|UniProtKB:P97333}.; ",{"$nulls":4},"p.Ile800Thr","c.2399T>C","MODERATE","800/923",16,{"$nulls":5},"4","521","441","368","309","461","386","0","0","0","0.0518",{"$nulls":20},"3.9391540000000003","4.32",".;2.075;.;2.075","1;0.999999;1;1","-2.12;-1.96;-1.96;-1.96","0.988;0.931;0.862;0.931","0.001","0.914;0.916;0.918;0.932",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","498,0","0","498","0/1","393,21","0.0507","414",null,"chr10:33185660:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0518"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NRP1","chr10:33185660","NRP1(I800T)",null,null,"topological domain (Extracellular ), domain (MAM ), splice variant (In isoform 2 and isoform 3. ), strand ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: The membrane-bound isoform 1 is a receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. It mediates the chemorepulsant activity of semaphorins. It binds to semaphorin 3A, The PLGF-2 isoform of PGF, The VEGF165 isoform of VEGFA and VEGFB. Coexpression with KDR results in increased VEGF165 binding to KDR as well as increased chemotaxis. Regulate VEGF-induced angiogenesis. Binding to VEGFA initiates a signaling pathway needed for motor neuron axon guidance and cell body migration, including for the caudal migration of facial motor neurons from rhombomere 4 to rhombomere 6 during embryonic development (By similarity). {ECO:0000250|UniProtKB:P97333}.; ",{"$nulls":4},"p.Ile800Thr","c.2399T>C","MODERATE","800/923",16,{"$nulls":5},"5","521","410","368","293","461","351","0","0","0","0.0712",{"$nulls":20},"3.9391540000000003","4.32",".;2.075;.;2.075","1;0.999999;1;1","-2.12;-1.96;-1.96;-1.96","0.988;0.931;0.862;0.931","0.001","0.914;0.916;0.918;0.932",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","511,0","0","511","0/1","378,26","0.0644","404",null,"chr10:33185660:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0683"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","NUP188","chr9:128998160","NUP188(M1121L)",{"$nulls":6},255,"PASS","Missense","rs775527707",6.056e-05,"DISEASE: Note=Copy number variations of NUP188 gene may be a cause of heterotaxy, a congenital heart disease resulting from abnormalities in left-right (LR) body patterning. {ECO:0000269|PubMed:21282601}.; ","FUNCTION: May function as a component of the nuclear pore complex (NPC).; ",{"$nulls":4},"p.Met1121Leu","c.3361A>T","MODERATE","1121/1749",31,{"$nulls":5},"5","687","557","503","398","558","448","0","0","0","0.1004",{"$nulls":20},"1.76261","1.64","0.895","0.999635","-0.72",null,"0.072","0.237",{"$nulls":3},"ExAC_SAS_AF",6.056e-05,{"$nulls":4},"The nuclear pore complex (NPC) is found on the nuclear envelope and forms a gateway that regulates the flow of proteins and RNAs between the cytoplasm and nucleoplasm. The NPC is comprised of approximately 30 distinct proteins collectively known as nucleoporins. Nucleoporins are pore-complex-specific glycoproteins which often have cytoplasmically oriented O-linked N-acetylglucosamine residues and numerous repeats of the pentapeptide sequence XFXFG. However, the nucleoporin protein encoded by this gene does not contain the typical FG repeat sequences found in most vertebrate nucleoporins. This nucleoporin is thought to form part of the scaffold for the central channel of the nuclear pore. [provided by RefSeq, Jan 2013].  ",null,"CN263352","0/0","652,0","0","652","0/1","466,46","0.0898","512",null,"chr9:128998160:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0955"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","NUP188","chr9:128998160","NUP188(M1121L)",{"$nulls":6},255,"PASS","Missense","rs775527707",6.056e-05,"DISEASE: Note=Copy number variations of NUP188 gene may be a cause of heterotaxy, a congenital heart disease resulting from abnormalities in left-right (LR) body patterning. {ECO:0000269|PubMed:21282601}.; ","FUNCTION: May function as a component of the nuclear pore complex (NPC).; ",{"$nulls":4},"p.Met1121Leu","c.3361A>T","MODERATE","1121/1749",31,{"$nulls":5},"5","687","498","503","359","558","408","0","0","0","0.1201",{"$nulls":20},"1.76261","1.64","0.895","0.999635","-0.72",null,"0.072","0.237",{"$nulls":3},"ExAC_SAS_AF",6.056e-05,{"$nulls":4},"The nuclear pore complex (NPC) is found on the nuclear envelope and forms a gateway that regulates the flow of proteins and RNAs between the cytoplasm and nucleoplasm. The NPC is comprised of approximately 30 distinct proteins collectively known as nucleoporins. Nucleoporins are pore-complex-specific glycoproteins which often have cytoplasmically oriented O-linked N-acetylglucosamine residues and numerous repeats of the pentapeptide sequence XFXFG. However, the nucleoporin protein encoded by this gene does not contain the typical FG repeat sequences found in most vertebrate nucleoporins. This nucleoporin is thought to form part of the scaffold for the central channel of the nuclear pore. [provided by RefSeq, Jan 2013].  ",null,"CN263352","0/0","654,0","0","654","0/1","410,58","0.1239","468",null,"chr9:128998160:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0947"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","OR11H6","chr14:20224372","OR11H6(N221K)",{"$nulls":6},255,"PASS","Missense","rs564813542",0.0001212,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn221Lys","c.663C>A","MODERATE","221/330",1,{"$nulls":5},"4","951","788","728","601","798","649","0.0011","0.0011","0","0.0724",{"$nulls":20},"1.883638","1.19","1.955","1","-1.7","0.407","0.003","0.272",{"$nulls":3},"ExAC_SAS_AF",0.0001212,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","931,2","0.0021","933","0/1","707,52","0.0685","759",null,"chr14:20224372:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0715"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","OR11H6","chr14:20224372","OR11H6(N221K)",{"$nulls":6},255,"PASS","Missense","rs564813542",0.0001212,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Asn221Lys","c.663C>A","MODERATE","221/330",1,{"$nulls":5},"4","951","653","728","502","802","552","0.0011","0.0011","0","0.0978",{"$nulls":20},"1.883638","1.19","1.955","1","-1.7","0.407","0.003","0.272",{"$nulls":3},"ExAC_SAS_AF",0.0001212,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","932,2","0.0021","934","0/1","567,67","0.1057","634",null,"chr14:20224372:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0996"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","OR2C1","chr16:3356562","OR2C1(A208P)",null,null,"transmembrane region (Helical; Name=5 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ala208Pro","c.622G>C","MODERATE","208/312",1,{"$nulls":5},"5","773","629","592","487","674","546","0","0","0","0.0788",{"$nulls":20},"3.096857","1.15","0.43","0.999992","-2.06","0.971","0.001","0.497",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","771,0","0","771","0/1","574,46","0.0742","620",null,"chr16:3356562:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0821"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","OR2Z1","chr19:8731776","OR2Z1(L250I)",null,null,"transmembrane region (Helical; Name=6 )",{"$nulls":3},255,"PASS","Missense","rs73489595",0.00226928895612708,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Leu250Ile","c.748C>A","MODERATE","250/314",1,{"$nulls":5},"4","727","596","608","477","636","503","0","0","0","0.0696",{"$nulls":20},"1.67452",".;8.42","1.17","0.999446",".;-1.32","1.0",".;0.14",".;0.092",{"$nulls":3},"1000Gp3_AFR_AF",0.00226928895612708,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","722,0","0","722","0/1","543,40","0.0686","583",null,"chr19:8731776:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0734"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","OR2Z1","chr19:8731776","OR2Z1(L250I)",null,null,"transmembrane region (Helical; Name=6 )",{"$nulls":3},255,"PASS","Missense","rs73489595",0.00226928895612708,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Leu250Ile","c.748C>A","MODERATE","250/314",1,{"$nulls":5},"4","727","516","608","417","634","443","0","0","0","0.0926",{"$nulls":20},"1.67452",".;8.42","1.17","0.999446",".;-1.32","1.0",".;0.14",".;0.092",{"$nulls":3},"1000Gp3_AFR_AF",0.00226928895612708,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","720,0","0","720","0/1","463,46","0.0904","509",null,"chr19:8731776:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0791"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","OR4C16","chr11:55572860","OR4C16(V245L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Val245Leu","c.733G>C","MODERATE","245/310",1,{"$nulls":5},"5","667","403","515","308","610","352","0","0","0","0.125",{"$nulls":20},"1.578656",null,"2.97","1",null,"0.996",{"$nulls":5},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","659,0","0","659","0/1","342,52","0.132","394",null,"chr11:55572860:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1201"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","OR5T1","chr11:56276413","OR5T1(G259*)",null,null,"transmembrane region (Helical; Name=6 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Gly259*","c.775G>T","HIGH","259/326",1,{"$nulls":5},"5","537","393","476","328","438","317","0","0","0","0.1073",{"$nulls":20},"6.591177",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","533,0","0","533","0/1","347,42","0.108","389",null,"chr11:56276413:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1189"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","OR5T1","chr11:56276413","OR5T1(G259*)",null,null,"transmembrane region (Helical; Name=6 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Gly259*","c.775G>T","HIGH","259/326",1,{"$nulls":5},"5","537","326","476","283","438","261","0","0","0","0.2107",{"$nulls":20},"6.591177",null,null,"1",{"$nulls":7},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","530,0","0","530","0/1","253,60","0.1917","313",null,"chr11:56276413:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1873"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","OR6N1","chr1:158766165","OR6N1(R173H)",{"$nulls":6},255,"PASS","Missense","rs760792253",6.9199999999999991E-4,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Arg173His","c.518G>A","MODERATE","173/312",1,2,{"$nulls":4},"4","339","278",null,null,"294","245","0","0","0","0.0612",{"$nulls":20},"-1.240572",".;8.73","0.12","1",".;-0.29","0.002",".;0.181",".;0.018",{"$nulls":3},"ExAC_AMR_AF",6.9199999999999991E-4,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","340,0","0","340","0/1","252,15","0.0562","267",null,"chr1:158766165:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","OR6N1","chr1:158766165","OR6N1(R173H)",{"$nulls":6},255,"PASS","Missense","rs760792253",6.9199999999999991E-4,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Arg173His","c.518G>A","MODERATE","173/312",1,2,{"$nulls":4},"5","339","199","292","167","294","168","0","0","0","0.0774",{"$nulls":20},"-1.240572",".;8.73","0.12","1",".;-0.29","0.002",".;0.181",".;0.018",{"$nulls":3},"ExAC_AMR_AF",6.9199999999999991E-4,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","340,0","0","340","0/1","182,14","0.0714","196",null,"chr1:158766165:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0778"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PAPSS2","chr10:87714983","PAPSS2(Splicing Acceptor/Donor Loss)",null,null,"region of interest (Adenylyl-sulfate kinase )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Bifunctional enzyme with both ATP sulfurylase and APS kinase activity, which mediates two steps in the sulfate activation pathway. The first step is the transfer of a sulfate group to ATP to yield adenosine 5'-phosphosulfate (APS), and the second step is the transfer of a phosphate group from ATP to APS yielding 3'-phosphoadenylylsulfate (PAPS: activated sulfate donor used by sulfotransferase). In mammals, PAPS is the sole source of sulfate; APS appears to be only an intermediate in the sulfate- activation pathway. May have a important role in skeletogenesis during postnatal growth (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asn214_Thr219del","c.640-1_654delGAACATTGTACCCTAT","HIGH","214/619",6,{"$nulls":5},"5","225","168","167","148","209","163","0","0","0","0.1411",{"$nulls":31},"Unknown",-1,"AR","Brachyolmia 4 with mild epiphyseal and metaphyseal changes","Endocrine; Musculoskeletal",{"$nulls":3},"C2748515","0/0","269,0","0","269","0/1","167,23","0.1211","190",null,"chr10:87714983:AGAACATTGTACCCTAT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1284"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PAPSS2","chr10:87714983","PAPSS2(Splicing Acceptor/Donor Loss)",null,null,"region of interest (Adenylyl-sulfate kinase )",{"$nulls":3},255,"PASS","Splice-site Loss",null,-1,null,"FUNCTION: Bifunctional enzyme with both ATP sulfurylase and APS kinase activity, which mediates two steps in the sulfate activation pathway. The first step is the transfer of a sulfate group to ATP to yield adenosine 5'-phosphosulfate (APS), and the second step is the transfer of a phosphate group from ATP to APS yielding 3'-phosphoadenylylsulfate (PAPS: activated sulfate donor used by sulfotransferase). In mammals, PAPS is the sole source of sulfate; APS appears to be only an intermediate in the sulfate- activation pathway. May have a important role in skeletogenesis during postnatal growth (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asn214_Thr219del","c.640-1_654delGAACATTGTACCCTAT","HIGH","214/619",6,{"$nulls":5},"5","225","154","167","134","209","143","0","0","0","0.1189",{"$nulls":31},"Unknown",-1,"AR","Brachyolmia 4 with mild epiphyseal and metaphyseal changes","Endocrine; Musculoskeletal",{"$nulls":3},"C2748515","0/0","269,0","0","269","0/1","165,19","0.1033","184",null,"chr10:87714983:AGAACATTGTACCCTAT:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.097"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PCSK2","chr20:17260326","PCSK2(Q88H)",null,null,"propeptide , splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the processing of hormone and other protein precursors at sites comprised of pairs of basic amino acid residues. Responsible for the release of glucagon from proglucagon in pancreatic A cells. {ECO:0000269|PubMed:28719828, ECO:0000269|PubMed:9287128}.; ",{"$nulls":4},"p.Gln88His","c.264G>T","MODERATE","88/638",2,1,{"$nulls":4},"4","137","159","99","107",null,null,"0","0",{"$nulls":22},"1.7003110000000001","1.56",".;0.375","0.750709;0.750709;1","-1.06;-0.85",".;0.0","0.164;0.159","0.245;0.253",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","138,0","0","138","0/1","149,10","0.0629","159",null,"chr20:17260326:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0654"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PCSK2","chr20:17260326","PCSK2(Q88H)",null,null,"propeptide , splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the processing of hormone and other protein precursors at sites comprised of pairs of basic amino acid residues. Responsible for the release of glucagon from proglucagon in pancreatic A cells. {ECO:0000269|PubMed:28719828, ECO:0000269|PubMed:9287128}.; ",{"$nulls":4},"p.Gln88His","c.264G>T","MODERATE","88/638",2,1,{"$nulls":4},"5","137","125","99","89","126","116","0","0","0","0.069",{"$nulls":20},"1.7003110000000001","1.56",".;0.375","0.750709;0.750709;1","-1.06;-0.85",".;0.0","0.164;0.159","0.245;0.253",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","135,0","0","135","0/1","113,10","0.0813","123",null,"chr20:17260326:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0787"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PDE1C","chr7:31816093","PDE1C(K608N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cyclic nucleotide phosphodiesterase with a dual- specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. Has a high affinity for both cAMP and cGMP.; ",{"$nulls":4},"p.Lys608Asn","c.1824G>T","MODERATE","608/769",16,{"$nulls":5},"4","550","540","363","357",null,null,"0","0",{"$nulls":22},"2.181219","-0.74;-0.72;-0.72;-0.7;-0.7",".;0.695;0.695;0.695;0.695","0.694824","-0.76",".;0.0;0.0;0.0;0.0","0.011;0.014;0.014;0.029;0.029","0.258;0.248;0.249;0.265;0.26",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748334","0/0","523,0","0","523","0/1","479,29","0.0571","508",null,"chr7:31816093:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.056"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PDE1C","chr7:31816093","PDE1C(K608N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Cyclic nucleotide phosphodiesterase with a dual- specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. Has a high affinity for both cAMP and cGMP.; ",{"$nulls":4},"p.Lys608Asn","c.1824G>T","MODERATE","608/769",16,{"$nulls":5},"5","550","458","363","305","497","406","0","0","0","0.069",{"$nulls":20},"2.181219","-0.74;-0.72;-0.72;-0.7;-0.7",".;0.695;0.695;0.695;0.695","0.694824","-0.76",".;0.0;0.0;0.0;0.0","0.011;0.014;0.014;0.029;0.029","0.258;0.248;0.249;0.265;0.26",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748334","0/0","523,0","0","523","0/1","398,30","0.0701","428",null,"chr7:31816093:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0787"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PHACTR4","chr1:28466399","PHACTR4(P162T)",null,null,"splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Regulator of protein phosphatase 1 (PP1) required for neural tube and optic fissure closure, and enteric neural crest cell (ENCCs) migration during development. Acts as an activator of PP1 by interacting with PPP1CA and preventing phosphorylation of PPP1CA at 'Thr-320'. During neural tube closure, localizes to the ventral neural tube and activates PP1, leading to down-regulate cell proliferation within cranial neural tissue and the neural retina. Also acts as a regulator of migration of enteric neural crest cells (ENCCs) by activating PP1, leading to dephosphorylation and subsequent activation of cofilin (COF1 or COF2) and repression of the integrin signaling through the RHO/ROCK pathway (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro162Thr","c.484C>A","MODERATE","162/712",5,{"$nulls":5},"5","500","314","401","259","404","266","0.002","0.002","0","0.0677",{"$nulls":20},"1.5496729999999999","1.16;.;1.16","2.28;.;.","0.998156","-4.92;.;-4.92","0.518;.;0.649","0.004;.;0.004","0.275;.;0.243",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","494,0","0","494","0/1","288,24","0.0769","312",null,"chr1:28466399:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0772"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PKHD1","chr6:52064997","PKHD1(R312W)",null,null,"topological domain (Extracellular ), domain (IPT/TIG 3 )",{"$nulls":3},255,"PASS","Missense","rs372340268",6.6619999999999993E-4,"DISEASE: Note=Loss-of-function PKHD1 variations may cause autosomal dominant polycystic liver disease (PCLD) in patients that lack variations in known causative genes, such as PRKCSH and SEC63. {ECO:0000269|PubMed:28375157}.; ","FUNCTION: May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation. {ECO:0000269|PubMed:20554582}.; ",{"$nulls":4},"p.Arg312Trp","c.934C>T","MODERATE","312/4074",13,{"$nulls":5},"5","204","140","138","93","182","128","0","0","0","0.1562",{"$nulls":20},"3.422817","-1.04","2.535","0.925556","-3.3;-3.33","1.0","0.004;0.003","0.492;0.506",{"$nulls":3},"ExAC_SAS_AF",6.6619999999999993E-4,"AR","Polycystic kidney disease, autosomal recessive","Allergy/Immunology/Infectious; Endocrine; Gastrointestinal; Renal",{"$nulls":3},"C0085548","0/0","208,0","0","208","0/1","122,22","0.1528","144",null,"chr6:52064997:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.172"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PKHD1","chr6:52064997","PKHD1(R312W)",null,null,"topological domain (Extracellular ), domain (IPT/TIG 3 )",{"$nulls":3},255,"PASS","Missense","rs372340268",6.6619999999999993E-4,"DISEASE: Note=Loss-of-function PKHD1 variations may cause autosomal dominant polycystic liver disease (PCLD) in patients that lack variations in known causative genes, such as PRKCSH and SEC63. {ECO:0000269|PubMed:28375157}.; ","FUNCTION: May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation. {ECO:0000269|PubMed:20554582}.; ",{"$nulls":4},"p.Arg312Trp","c.934C>T","MODERATE","312/4074",13,{"$nulls":5},"5","204","161","138","108","182","141","0","0","0","0.1631",{"$nulls":20},"3.422817","-1.04","2.535","0.925556","-3.3;-3.33","1.0","0.004;0.003","0.492;0.506",{"$nulls":3},"ExAC_SAS_AF",6.6619999999999993E-4,"AR","Polycystic kidney disease, autosomal recessive","Allergy/Immunology/Infectious; Endocrine; Gastrointestinal; Renal",{"$nulls":3},"C0085548","0/0","208,0","0","208","0/1","136,28","0.1707","164",null,"chr6:52064997:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1944"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PLEKHG2","chr19:39423440","PLEKHG2(L796V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Leukodystrophy and acquired microcephaly with or without dystonia (LDAMD) [MIM:616763]: An autosomal recessive neurologic disorder characterized by profound mental retardation, dystonia, postnatal microcephaly, and white matter abnormalities consistent with leukodystrophy. {ECO:0000269|PubMed:26573021}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a transforming oncogene with exchange activity for CDC42 (By similarity). May be a guanine-nucleotide exchange factor (GEF) for RAC1 and CDC42. Activated by the binding to subunits beta and gamma of the heterotrimeric guanine nucleotide- binding protein (G protein) (PubMed:18045877). Involved in the regulation of actin polymerization (PubMed:26573021). {ECO:0000250|UniProtKB:Q6KAU7, ECO:0000269|PubMed:18045877, ECO:0000269|PubMed:26573021}.; ",{"$nulls":4},"p.Leu796Val","c.2386C>G","MODERATE","796/1386",18,{"$nulls":5},"5","670","624","525","482","609","532","0","0","0","0.0714",{"$nulls":20},"3.220543",".;-1.24;.","1.545;.;.","1;1;0.92927;0.92927;0.92927",".;-1.45;.","0.993;0.99;.",".;0.0;.","0.492;0.44;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225213","0/0","665,0","0","665","0/1","564,47","0.0769","611",null,"chr19:39423440:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0768"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PLEKHG2","chr19:39423440","PLEKHG2(L796V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Leukodystrophy and acquired microcephaly with or without dystonia (LDAMD) [MIM:616763]: An autosomal recessive neurologic disorder characterized by profound mental retardation, dystonia, postnatal microcephaly, and white matter abnormalities consistent with leukodystrophy. {ECO:0000269|PubMed:26573021}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May be a transforming oncogene with exchange activity for CDC42 (By similarity). May be a guanine-nucleotide exchange factor (GEF) for RAC1 and CDC42. Activated by the binding to subunits beta and gamma of the heterotrimeric guanine nucleotide- binding protein (G protein) (PubMed:18045877). Involved in the regulation of actin polymerization (PubMed:26573021). {ECO:0000250|UniProtKB:Q6KAU7, ECO:0000269|PubMed:18045877, ECO:0000269|PubMed:26573021}.; ",{"$nulls":4},"p.Leu796Val","c.2386C>G","MODERATE","796/1386",18,{"$nulls":5},"5","670","602","525","451","609","527","0","0","0","0.1082",{"$nulls":20},"3.220543",".;-1.24;.","1.545;.;.","1;1;0.92927;0.92927;0.92927",".;-1.45;.","0.993;0.99;.",".;0.0;.","0.492;0.44;.",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225213","0/0","667,0","0","667","0/1","521,63","0.1079","584",null,"chr19:39423440:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1042"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PMM2","chr16:8847751","PMM2(D223H)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Congenital disorder of glycosylation 1A (CDG1A) [MIM:212065]: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. CDG1A is an autosomal recessive disorder characterized by a severe encephalopathy with axial hypotonia, abnormal eye movement, and pronounced psychomotor retardation, as well as peripheral neuropathy, cerebellar hypoplasia, and retinitis pigmentosa. Patients show a peculiar distribution of subcutaneous fat, nipple retraction, and hypogonadism. {ECO:0000269|PubMed:10066032, ECO:0000269|PubMed:10527672, ECO:0000269|PubMed:10571956, ECO:0000269|PubMed:10602363, ECO:0000269|PubMed:10801058, ECO:0000269|PubMed:11058895, ECO:0000269|PubMed:11058896, ECO:0000269|PubMed:11350185, ECO:0000269|PubMed:12357336, ECO:0000269|PubMed:15844218, ECO:0000269|PubMed:17307006, ECO:0000269|PubMed:9140401, ECO:0000269|PubMed:9497260, ECO:0000269|PubMed:9781039}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions. {ECO:0000250}.; ",{"$nulls":4},"p.Asp223His","c.667G>C","MODERATE","223/246",8,{"$nulls":5},"5","660","691","485","495","575","590","0","0","0","0.061",{"$nulls":20},"3.888601","-5.06",".;2.33;.","1","-5.39;-5.23;-5.62",".;0.954;.","0.212;0.17;0.128","0.924;0.844;0.866",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type Ia","Biochemical; Cardiovascular; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C0349653","0/0","637,0","0","637","0/1","623,44","0.066","667",null,"chr16:8847751:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0626"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PPP1R3F","chrX:49286467","PPP1R3F(D593N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Glycogen-targeting subunit for protein phosphatase 1 (PP1). {ECO:0000269|PubMed:21668450}.; ",{"$nulls":4},"p.Asp593Asn","c.1777G>A","MODERATE","593/799",4,{"$nulls":5},"5","1164","913","927","687","1044","791","0","0","0","0.067",{"$nulls":20},"3.075883","0.56;0.11;0.56;0.56",".;1.895;.;.","0.980041;0.987885;0.980041;0.980041;0.980041","-4.66;-1.39;-4.66;-4.66",".;0.89;.;.","0.086;0.057;0.086;0.086","0.209;0.134;0.249;0.209",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1129,0","0","1129","0/1","824,59","0.0668","883",null,"chrX:49286467:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0568"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PPP1R3F","chrX:49286467","PPP1R3F(D593N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Glycogen-targeting subunit for protein phosphatase 1 (PP1). {ECO:0000269|PubMed:21668450}.; ",{"$nulls":4},"p.Asp593Asn","c.1777G>A","MODERATE","593/799",4,{"$nulls":5},"5","1164","769","927","600","1043","674","0","0","0","0.0875",{"$nulls":20},"3.075883","0.56;0.11;0.56;0.56",".;1.895;.;.","0.980041;0.987885;0.980041;0.980041;0.980041","-4.66;-1.39;-4.66;-4.66",".;0.89;.;.","0.086;0.057;0.086;0.086","0.209;0.134;0.249;0.209",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1140,0","0","1140","0/1","677,71","0.0949","748",null,"chrX:49286467:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0967"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PPT1","chr1:40074134","PPT1(L283P)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Ceroid lipofuscinosis, neuronal, 1 (CLN1) [MIM:256730]: A form of neuronal ceroid lipofuscinosis with variable age at onset. Infantile, late-infantile, juvenile, and adult onset have been reported. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. The lipopigment pattern seen most often in CLN1 is referred to as granular osmiophilic deposits (GROD). {ECO:0000269|PubMed:11506414, ECO:0000269|PubMed:19201763, ECO:0000269|PubMed:19941651, ECO:0000269|PubMed:21990111, ECO:0000269|PubMed:7637805, ECO:0000269|PubMed:9425237, ECO:0000269|PubMed:9664077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Removes thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosomal degradation. Prefers acyl chain lengths of 14 to 18 carbons (PubMed:8816748). {ECO:0000269|PubMed:8816748}.; ","epilepsy",{"$nulls":4},"c.848T>C","HIGH",null,9,{"$nulls":5},"4","604","476","446","319","523","400","0","0","0","0.0725",{"$nulls":20},"4.217814",".;.;-4.56;.;.;-4.56;.","3.61;.;.;.;.;.;.","1",".;.;-6.62;.;.;-6.58;.","1.0;.;.;.;.;1.0;.",".;.;0.001;.;.;0.003;.",".;.;0.956;.;.;0.921;.",{"$nulls":3},"Unknown",-1,"AR","Ceroid lipofuscinosis, neuronal, 1","Biochemical; Neurologic; Ophthalmologic",{"$nulls":3},"C1850451","0/0","572,0","0","572","0/1","412,32","0.0721","444",null,"chr1:40074134:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.069"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PPT1","chr1:40074134","PPT1(L283P)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Ceroid lipofuscinosis, neuronal, 1 (CLN1) [MIM:256730]: A form of neuronal ceroid lipofuscinosis with variable age at onset. Infantile, late-infantile, juvenile, and adult onset have been reported. Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterized by intracellular accumulation of autofluorescent liposomal material, and clinically by seizures, dementia, visual loss, and/or cerebral atrophy. The lipopigment pattern seen most often in CLN1 is referred to as granular osmiophilic deposits (GROD). {ECO:0000269|PubMed:11506414, ECO:0000269|PubMed:19201763, ECO:0000269|PubMed:19941651, ECO:0000269|PubMed:21990111, ECO:0000269|PubMed:7637805, ECO:0000269|PubMed:9425237, ECO:0000269|PubMed:9664077}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Removes thioester-linked fatty acyl groups such as palmitate from modified cysteine residues in proteins or peptides during lysosomal degradation. Prefers acyl chain lengths of 14 to 18 carbons (PubMed:8816748). {ECO:0000269|PubMed:8816748}.; ","epilepsy",{"$nulls":4},"c.848T>C","HIGH",null,9,{"$nulls":5},"4","604","422","446","296","520","367","0","0","0","0.1008",{"$nulls":20},"4.217814",".;.;-4.56;.;.;-4.56;.","3.61;.;.;.;.;.;.","1",".;.;-6.62;.;.;-6.58;.","1.0;.;.;.;.;1.0;.",".;.;0.001;.;.;0.003;.",".;.;0.956;.;.;0.921;.",{"$nulls":3},"Unknown",-1,"AR","Ceroid lipofuscinosis, neuronal, 1","Biochemical; Neurologic; Ophthalmologic",{"$nulls":3},"C1850451","0/0","571,0","0","571","0/1","363,41","0.1015","404",null,"chr1:40074134:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1014"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PRPH","chr12:49295632","PRPH(C144*)",null,null,"domain (IF rod ), region of interest (Coil 1B )","miscellaneous-region:Coil_1B","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Class-III neuronal intermediate filament protein.; ",{"$nulls":4},"p.Cys144*","c.432C>A","HIGH","144/470",1,{"$nulls":5},"4","289","223","226","181","230","183","0","0","0","0.1038",{"$nulls":5},"(PRPH|ENSG00000135406|1|1.00)","(PRPH|ENSG00000135406|1|1.00)",{"$nulls":13},"7.381253",null,null,"1",{"$nulls":3},"0.768",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1862939","0/0","285,0","0","285","0/1","196,23","0.105","219",null,"chr12:49295632:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1215"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PRPH","chr12:49295632","PRPH(C144*)",null,null,"domain (IF rod ), region of interest (Coil 1B )","miscellaneous-region:Coil_1B","LOW",null,255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Class-III neuronal intermediate filament protein.; ",{"$nulls":4},"p.Cys144*","c.432C>A","HIGH","144/470",1,{"$nulls":5},"4","289","171","226","138","230","137","0","0","0","0.0949",{"$nulls":5},"(PRPH|ENSG00000135406|1|1.00)","(PRPH|ENSG00000135406|1|1.00)",{"$nulls":13},"7.381253",null,null,"1",{"$nulls":3},"0.768",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C1862939","0/0","284,0","0","284","0/1","156,14","0.0824","170",null,"chr12:49295632:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.087"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PRSS21","chr16:2817442","PRSS21(A26V)",null,null,"propeptide ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Could regulate proteolytic events associated with testicular germ cell maturation.; ",{"$nulls":4},"p.Ala26Val","c.77C>T","MODERATE","26/314",2,{"$nulls":5},"5","82","88","60","61","79","80","0","0","0","0.075",{"$nulls":20},"-1.335935","-1.5","0.69","1","-0.47;-0.43","0.001;0.0","0.303;0.229","0.084;0.048",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","58,0","0","58","0/1","60,6","0.0909","66",null,"chr16:2817442:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.082"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","PRSS27","chr16:2714074","PRSS27(G162fs)",null,null,"domain (Peptidase S1 ), disulfide bond ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gly162fs","c.483_498delTGGCTGGGGCAGCCCC","HIGH","161/290",4,{"$nulls":5},"5","245","228","225","206","247","228","0","0","0","0.1886",{"$nulls":5},"(PRSS27|ENSG00000172382|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","303,0","0","303","0/1","231,45","0.163","276",null,"chr16:2714074:TGGGGCTGCCCCAGCCA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.199"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","PRSS27","chr16:2714074","PRSS27(G162fs)",null,null,"domain (Peptidase S1 ), disulfide bond ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gly162fs","c.483_498delTGGCTGGGGCAGCCCC","HIGH","161/290",4,{"$nulls":5},"5","245","199","225","184","247","206","0","0","0","0.1505",{"$nulls":5},"(PRSS27|ENSG00000172382|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","303,0","0","303","0/1","220,35","0.1373","255",null,"chr16:2714074:TGGGGCTGCCCCAGCCA:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1793"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RAD54B","chr8:94391893","RAD54B(K509Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in DNA repair and mitotic recombination. May play an active role in recombination processes in concert with other members of the RAD52 epistasis group. {ECO:0000269|PubMed:11782437, ECO:0000269|PubMed:11884632}.; ","level2",{"$nulls":3},"p.Lys509Gln","c.1525A>C","MODERATE","509/910",10,{"$nulls":5},"5","187","177","133","127","177","166","0","0","0","0.0964",{"$nulls":20},"1.950657","-3.15;.","0.93;.","0.718709","-1.94;.","0.119;.","0.221;.","0.187;0.181",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kHOMOLOGOUS_RECOMBINATION",null,null,"C4721532| C1527249","0/0","185,0","0","185","0/1","157,18","0.1029","175",null,"chr8:94391893:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0945"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","RARS","chr5:168500629","RARS(K287N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Leukodystrophy, hypomyelinating, 9 (HLD9) [MIM:616140]: An autosomal recessive neurodegenerative disorder characterized by delayed psychomotor development, severe spasticity, nystagmus, and ataxia associated with diffuse hypomyelination apparent on brain MRI. {ECO:0000269|PubMed:24777941}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis (PubMed:25288775). Modulates the secretion of AIMP1 and may be involved in generation of the inflammatory cytokine EMAP2 from AIMP1 (PubMed:17443684). {ECO:0000269|PubMed:17443684, ECO:0000269|PubMed:25288775}.; ","mitocarta",{"$nulls":3},"p.Lys287Asn","c.861G>C","MODERATE","287/660",8,{"$nulls":5},"3","348","294",{"$nulls":4},"0.0029","0.0029",{"$nulls":22},"3.638483","-0.07","2.31","1","-4.3","0.921","0.024","0.814",{"$nulls":3},"Unknown",-1,"AD","Leukodystrophy, hypomyelinating 9","Neurologic",null,"Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Arginyl-tRNA synthetase belongs to the class-I aminoacyl-tRNA synthetase family. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","345,1","0.0029","346","0/1","272,16","0.0556","288",null,"chr5:168500629:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RARS","chr5:168500629","RARS(K287N)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Leukodystrophy, hypomyelinating, 9 (HLD9) [MIM:616140]: An autosomal recessive neurodegenerative disorder characterized by delayed psychomotor development, severe spasticity, nystagmus, and ataxia associated with diffuse hypomyelination apparent on brain MRI. {ECO:0000269|PubMed:24777941}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Forms part of a macromolecular complex that catalyzes the attachment of specific amino acids to cognate tRNAs during protein synthesis (PubMed:25288775). Modulates the secretion of AIMP1 and may be involved in generation of the inflammatory cytokine EMAP2 from AIMP1 (PubMed:17443684). {ECO:0000269|PubMed:17443684, ECO:0000269|PubMed:25288775}.; ","mitocarta",{"$nulls":3},"p.Lys287Asn","c.861G>C","MODERATE","287/660",8,{"$nulls":5},"3","348","257",{"$nulls":4},"0.0029","0.0029",{"$nulls":22},"3.638483","-0.07","2.31","1","-4.3","0.921","0.024","0.814",{"$nulls":3},"Unknown",-1,"AD","Leukodystrophy, hypomyelinating 9","Neurologic",null,"Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Arginyl-tRNA synthetase belongs to the class-I aminoacyl-tRNA synthetase family. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","340,1","0.0029","341","0/1","232,18","0.072","250",null,"chr5:168500629:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","RBM44","chr2:237827268","RBM44(P824H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of intercellular bridges during meiosis. Intercellular bridges are evolutionarily conserved structures that connect differentiating germ cells. Not required for fertility (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro824His","c.2471C>A","MODERATE","824/1052",11,{"$nulls":5},"4","235","200","190","163","190","147","0","0","0","0.1429",{"$nulls":20},"2.660033","2.22;2.22;.",null,"1","-3.98;-3.98;.",null,"0.119;0.119;.","0.211;0.263;0.177",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","228,0","0","228","0/1","167,28","0.1436","195",null,"chr2:237827268:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1411"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RBM44","chr2:237827268","RBM44(P824H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of intercellular bridges during meiosis. Intercellular bridges are evolutionarily conserved structures that connect differentiating germ cells. Not required for fertility (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro824His","c.2471C>A","MODERATE","824/1052",11,{"$nulls":5},"4","235","198","190","151","192","159","0","0","0","0.2075",{"$nulls":20},"2.660033","2.22;2.22;.",null,"1","-3.98;-3.98;.",null,"0.119;0.119;.","0.211;0.263;0.177",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","228,0","0","228","0/1","159,37","0.1888","196",null,"chr2:237827268:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1788"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","RFX4","chr12:106761308","RFX4(T692P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. {ECO:0000250|UniProtKB:Q7TNK1}.; ",{"$nulls":4},"p.Thr692Pro","c.2074A>C","MODERATE","692/744",18,{"$nulls":5},"4","555","517","420","385","479","428","0","0","0","0.0771",{"$nulls":20},"1.724736","1.3","0;.;.","0.649536","-1.04;-1.04;-0.76","0.079;0.0;.","0.04;0.036;0.033","0.081;0.16;0.187",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","546,0","0","546","0/1","456,39","0.0788","495",null,"chr12:106761308:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0805"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RFX4","chr12:106761308","RFX4(T692P)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development. {ECO:0000250|UniProtKB:Q7TNK1}.; ",{"$nulls":4},"p.Thr692Pro","c.2074A>C","MODERATE","692/744",18,{"$nulls":5},"4","555","386","420","291","480","325","0","0","0","0.0954",{"$nulls":20},"1.724736","1.3","0;.;.","0.649536","-1.04;-1.04;-0.76","0.079;0.0;.","0.04;0.036;0.033","0.081;0.16;0.187",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","548,0","0","548","0/1","341,37","0.0979","378",null,"chr12:106761308:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0997"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","RIPK4","chr21:41745892","RIPK4(R316fs)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Popliteal pterygium syndrome, lethal type (PPS-L) [MIM:263650]: An autosomal recessive disorder characterized by multiple popliteal pterygia leading to severe arthrogryposis, ankyloblepharon filiforme adnatum, filiform bands between the jaws, synostosis of the carpal/tarsal and phalangeal bones in the hands and feet, digital hypoplasia/aplasia, complete soft-tissue syndactyly, lack of nails, lack of scalp hair, eyebrows and eyelashes, blepharophimosis, cleft lip and/or palate, and hypoplastic external genitalia. Early lethality is common, although survival into childhood and beyond has been reported. {ECO:0000269|PubMed:22197488, ECO:0000269|PubMed:22197489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in stratified epithelial development. It is a direct transcriptional target of TP63. Plays a role in NF-kappa-B activation. {ECO:0000269|PubMed:12446564, ECO:0000269|PubMed:22197488}.; ",{"$nulls":4},"p.Arg316fs","c.935-2_946dupAGAAGTCATCATCC","HIGH","316/832",7,{"$nulls":5},"4",null,null,"366","298","431","397",null,null,"0","0.0882",{"$nulls":5},"(RIPK4|ENSG00000183421|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Popliteal pterygium syndrome, lethal type; Bartsocas-Papas syndrome ","Craniofacial; Dermatologic; Genitourinary; Musculoskeletal; Ophthalmologic",{"$nulls":3},"C0406733| C1849718","0/0","394,0","0","543","0/1","293,43","0.128","450",null,"chr21:41745892:C:CGGATGATGACTTCT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1141"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RIPK4","chr21:41745892","RIPK4(R316fs)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Popliteal pterygium syndrome, lethal type (PPS-L) [MIM:263650]: An autosomal recessive disorder characterized by multiple popliteal pterygia leading to severe arthrogryposis, ankyloblepharon filiforme adnatum, filiform bands between the jaws, synostosis of the carpal/tarsal and phalangeal bones in the hands and feet, digital hypoplasia/aplasia, complete soft-tissue syndactyly, lack of nails, lack of scalp hair, eyebrows and eyelashes, blepharophimosis, cleft lip and/or palate, and hypoplastic external genitalia. Early lethality is common, although survival into childhood and beyond has been reported. {ECO:0000269|PubMed:22197488, ECO:0000269|PubMed:22197489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in stratified epithelial development. It is a direct transcriptional target of TP63. Plays a role in NF-kappa-B activation. {ECO:0000269|PubMed:12446564, ECO:0000269|PubMed:22197488}.; ",{"$nulls":4},"p.Arg316fs","c.935-2_946dupAGAAGTCATCATCC","HIGH","316/832",7,{"$nulls":5},"4",null,null,"366","260","432","323",null,null,"0","0.0991",{"$nulls":5},"(RIPK4|ENSG00000183421|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Popliteal pterygium syndrome, lethal type; Bartsocas-Papas syndrome ","Craniofacial; Dermatologic; Genitourinary; Musculoskeletal; Ophthalmologic",{"$nulls":3},"C0406733| C1849718","0/0","394,0","0","543","0/1","224,38","0.145","380",null,"chr21:41745892:C:CGGATGATGACTTCT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1115"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","RPS6","chr9:19376615","RPS6(R178H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.; ","level2",{"$nulls":3},"p.Arg178His","c.533G>A","MODERATE","178/249",5,{"$nulls":5},"5","439","383","314","269","401","346","0","0","0","0.0751",{"$nulls":20},"3.021088","0.49;0.47;0.47","1.215;.;.","1","-4.04","0.366;.;.","0.079;0.085;0.085","0.697;0.69;0.69",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMTOR",{"$nulls":3},"0/0","432,0","0","432","0/1","338,31","0.084","369",null,"chr9:19376615:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0818"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RPS6","chr9:19376615","RPS6(R178H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.; ","level2",{"$nulls":3},"p.Arg178His","c.533G>A","MODERATE","178/249",5,{"$nulls":5},"5","439","392","314","269","402","347","0","0","0","0.0663",{"$nulls":20},"3.021088","0.49;0.47;0.47","1.215;.;.","1","-4.04","0.366;.;.","0.079;0.085;0.085","0.697;0.69;0.69",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMTOR",{"$nulls":3},"0/0","433,0","0","433","0/1","357,26","0.0679","383",null,"chr9:19376615:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0781"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","RTL1","chr14:100882092","RTL1(K899N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta. {ECO:0000250}.; ",{"$nulls":4},"p.Lys899Asn","c.2697G>T","MODERATE","899/1358",1,{"$nulls":5},"4","885","694","725","539","777","598","0","0","0","0.0786",{"$nulls":20},"1.052129",".;0.94","2.045","1",".;-3.67",null,".;0.023",".;0.165",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009].  ",null,null,"0/0","875,0","0","875","0/1","617,53","0.0791","670",null,"chr14:100882092:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0798"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","RTL1","chr14:100882092","RTL1(K899N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface and for development of the placenta. {ECO:0000250}.; ",{"$nulls":4},"p.Lys899Asn","c.2697G>T","MODERATE","899/1358",1,{"$nulls":5},"4","885","555","725","444","778","492","0","0","0","0.0833",{"$nulls":20},"1.052129",".;0.94","2.045","1",".;-3.67",null,".;0.023",".;0.165",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009].  ",null,null,"0/0","878,0","0","878","0/1","492,46","0.0855","538",null,"chr14:100882092:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0923"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SACS","chr13:23340037","SACS(K1267_W1279del)",{"$nulls":6},255,"PASS","Inframe Indel",null,-1,"DISEASE: Spastic ataxia Charlevoix-Saguenay type (SACS) [MIM:270550]: A neurodegenerative disease characterized by early- onset cerebellar ataxia, spasticity, retinal hypermyelination, pyramidal signs, and both axonal and demyelinating neuropathy with loss of sensory nerve conduction and reduced motor conduction velocities. Other features include dysarthria, distal muscle wasting, nystagmus, defect in conjugate pursuit ocular movements, retinal striation (from prominent retinal nerves) obscuring the retinal blood vessels in places, and the frequent presence of mitral valve prolapse. {ECO:0000269|PubMed:10655055, ECO:0000269|PubMed:12873855, ECO:0000269|PubMed:14718708, ECO:0000269|PubMed:15156359, ECO:0000269|PubMed:15985586, ECO:0000269|PubMed:16007637, ECO:0000269|PubMed:17290461, ECO:0000269|PubMed:17716690, ECO:0000269|PubMed:18398442, ECO:0000269|PubMed:18465152, ECO:0000269|PubMed:18484239, ECO:0000269|PubMed:19529988, ECO:0000269|PubMed:20876471, ECO:0000269|PubMed:27133561}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Co-chaperone which acts as a regulator of the Hsp70 chaperone machinery and may be involved in the processing of other ataxia-linked proteins. {ECO:0000269|PubMed:19208651}.; ","gedi",{"$nulls":3},"p.Lys1267_Trp1279del","c.3800_3838delAAGATTCTTTTAGAGCCTTAAAATTTCCATGGGTTTGGA","MODERATE","1267/4579",9,{"$nulls":5},"4",null,null,"332","231","348","219",null,null,"0","0.0868",{"$nulls":31},"Unknown",-1,"AR","Spastic ataxia, Charlevoix-Saguenay type","Cardiovascular; Musculoskeletal;  Neurologic; Ophthalmologic",null,"This gene encodes the sacsin protein, which includes a UbL domain at the N-terminus, a DnaJ domain, and a HEPN domain at the C-terminus. The gene is highly expressed in the central nervous system, also found in skin, skeletal muscles and at low levels in the pancreas. This gene includes a very large exon spanning more than 12.8 kb. Mutations in this gene result in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), a neurodegenerative disorder characterized by early-onset cerebellar ataxia with spasticity and peripheral neuropathy. The authors of a publication on the effects of siRNA-mediated sacsin knockdown concluded that sacsin protects against mutant ataxin-1 and suggest that 'the large multi-domain sacsin protein is able to recruit Hsp70 chaperone action and has the potential to regulate the effects of other ataxia proteins' (Parfitt et al., PubMed: 19208651). A pseudogene associated with this gene is located on chromosome 11. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013].",null,"C1849140","0/0","570,0","0","570","0/1","340,23","0.0634","363",null,"chr13:23340037:GTCCAAACCCATGGAAATTTTAAGGCTCTAAAAGAATCTT:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0779"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SACS","chr13:23339570","SACS(V1436L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spastic ataxia Charlevoix-Saguenay type (SACS) [MIM:270550]: A neurodegenerative disease characterized by early- onset cerebellar ataxia, spasticity, retinal hypermyelination, pyramidal signs, and both axonal and demyelinating neuropathy with loss of sensory nerve conduction and reduced motor conduction velocities. Other features include dysarthria, distal muscle wasting, nystagmus, defect in conjugate pursuit ocular movements, retinal striation (from prominent retinal nerves) obscuring the retinal blood vessels in places, and the frequent presence of mitral valve prolapse. {ECO:0000269|PubMed:10655055, ECO:0000269|PubMed:12873855, ECO:0000269|PubMed:14718708, ECO:0000269|PubMed:15156359, ECO:0000269|PubMed:15985586, ECO:0000269|PubMed:16007637, ECO:0000269|PubMed:17290461, ECO:0000269|PubMed:17716690, ECO:0000269|PubMed:18398442, ECO:0000269|PubMed:18465152, ECO:0000269|PubMed:18484239, ECO:0000269|PubMed:19529988, ECO:0000269|PubMed:20876471, ECO:0000269|PubMed:27133561}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Co-chaperone which acts as a regulator of the Hsp70 chaperone machinery and may be involved in the processing of other ataxia-linked proteins. {ECO:0000269|PubMed:19208651}.; ","gedi",{"$nulls":3},"p.Val1436Leu","c.4306G>C","MODERATE","1436/4579",9,{"$nulls":5},"4","467","315","361","251","417","278","0","0","0","0.0647",{"$nulls":20},"2.832229","-3.28",".;0.805","0.999637","-1.23;-1.27",".;0.091","0.167;0.154","0.847;0.851",{"$nulls":3},"Unknown",-1,"AR","Spastic ataxia, Charlevoix-Saguenay type","Cardiovascular; Musculoskeletal;  Neurologic; Ophthalmologic",null,"This gene encodes the sacsin protein, which includes a UbL domain at the N-terminus, a DnaJ domain, and a HEPN domain at the C-terminus. The gene is highly expressed in the central nervous system, also found in skin, skeletal muscles and at low levels in the pancreas. This gene includes a very large exon spanning more than 12.8 kb. Mutations in this gene result in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), a neurodegenerative disorder characterized by early-onset cerebellar ataxia with spasticity and peripheral neuropathy. The authors of a publication on the effects of siRNA-mediated sacsin knockdown concluded that sacsin protects against mutant ataxin-1 and suggest that 'the large multi-domain sacsin protein is able to recruit Hsp70 chaperone action and has the potential to regulate the effects of other ataxia proteins' (Parfitt et al., PubMed: 19208651). A pseudogene associated with this gene is located on chromosome 11. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013].",null,"C1849140","0/0","461,0","0","461","0/1","289,20","0.0647","309",null,"chr13:23339570:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0677"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SACS","chr13:23339570","SACS(V1436L)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Spastic ataxia Charlevoix-Saguenay type (SACS) [MIM:270550]: A neurodegenerative disease characterized by early- onset cerebellar ataxia, spasticity, retinal hypermyelination, pyramidal signs, and both axonal and demyelinating neuropathy with loss of sensory nerve conduction and reduced motor conduction velocities. Other features include dysarthria, distal muscle wasting, nystagmus, defect in conjugate pursuit ocular movements, retinal striation (from prominent retinal nerves) obscuring the retinal blood vessels in places, and the frequent presence of mitral valve prolapse. {ECO:0000269|PubMed:10655055, ECO:0000269|PubMed:12873855, ECO:0000269|PubMed:14718708, ECO:0000269|PubMed:15156359, ECO:0000269|PubMed:15985586, ECO:0000269|PubMed:16007637, ECO:0000269|PubMed:17290461, ECO:0000269|PubMed:17716690, ECO:0000269|PubMed:18398442, ECO:0000269|PubMed:18465152, ECO:0000269|PubMed:18484239, ECO:0000269|PubMed:19529988, ECO:0000269|PubMed:20876471, ECO:0000269|PubMed:27133561}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Co-chaperone which acts as a regulator of the Hsp70 chaperone machinery and may be involved in the processing of other ataxia-linked proteins. {ECO:0000269|PubMed:19208651}.; ","gedi",{"$nulls":3},"p.Val1436Leu","c.4306G>C","MODERATE","1436/4579",9,{"$nulls":5},"4","467","288","361","216","417","244","0","0","0","0.0902",{"$nulls":20},"2.832229","-3.28",".;0.805","0.999637","-1.23;-1.27",".;0.091","0.167;0.154","0.847;0.851",{"$nulls":3},"Unknown",-1,"AR","Spastic ataxia, Charlevoix-Saguenay type","Cardiovascular; Musculoskeletal;  Neurologic; Ophthalmologic",null,"This gene encodes the sacsin protein, which includes a UbL domain at the N-terminus, a DnaJ domain, and a HEPN domain at the C-terminus. The gene is highly expressed in the central nervous system, also found in skin, skeletal muscles and at low levels in the pancreas. This gene includes a very large exon spanning more than 12.8 kb. Mutations in this gene result in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), a neurodegenerative disorder characterized by early-onset cerebellar ataxia with spasticity and peripheral neuropathy. The authors of a publication on the effects of siRNA-mediated sacsin knockdown concluded that sacsin protects against mutant ataxin-1 and suggest that 'the large multi-domain sacsin protein is able to recruit Hsp70 chaperone action and has the potential to regulate the effects of other ataxia proteins' (Parfitt et al., PubMed: 19208651). A pseudogene associated with this gene is located on chromosome 11. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013].",null,"C1849140","0/0","463,0","0","463","0/1","251,28","0.1004","279",null,"chr13:23339570:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1065"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SCAI","chr9:125143407","SCAI(P11T)",null,null,"region of interest (Necessary to inhibit MRTFA-induced SRF transcriptional activity )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Tumor suppressor which functions to suppress MRTFA- induced SRF transcriptional activity. May function in the RHOA- DIAPH1 signal transduction pathway and regulate cell migration through transcriptional regulation of ITGB1. {ECO:0000269|PubMed:19350017}.; ",{"$nulls":4},"p.Pro11Thr","c.31C>A","MODERATE","11/629",1,{"$nulls":5},"5","62","52","41","34","53","38","0","0","0","0.1316",{"$nulls":20},"3.024483","0.91;0.3","0.205","0.926726","0.15;0.05","0.005;0.023","0.0","0.349;0.361",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","53,0","0","53","0/1","35,3","0.0789","38",null,"chr9:125143407:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1471"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SCLY","chr2:238069324","SCLY(V119L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the decomposition of L-selenocysteine to L- alanine and elemental selenium. {ECO:0000250}.; ",{"$nulls":4},"p.Val119Leu","c.355G>T","MODERATE","119/453",4,{"$nulls":5},"5","605","465","486","364","438","339","0","0","0","0.1209",{"$nulls":20},"1.6905160000000001","2.04;1.65;-2.06",".;0.485;.","0.767355;0.767355;0.767355;0.999999;0.999999","-1.02;-1.04;-0.68",".;0.002;.","0.453;0.412;0.402","0.228;0.226;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","595,0","0","595","0/1","399,51","0.1133","450",null,"chr2:238069324:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1126"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SCLY","chr2:238069324","SCLY(V119L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Catalyzes the decomposition of L-selenocysteine to L- alanine and elemental selenium. {ECO:0000250}.; ",{"$nulls":4},"p.Val119Leu","c.355G>T","MODERATE","119/453",4,{"$nulls":5},"5","605","376","486","300","438","284","0","0","0","0.1655",{"$nulls":20},"1.6905160000000001","2.04;1.65;-2.06",".;0.485;.","0.767355;0.767355;0.767355;0.999999;0.999999","-1.02;-1.04;-0.68",".;0.002;.","0.453;0.412;0.402","0.228;0.226;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","595,0","0","595","0/1","308,56","0.1538","364",null,"chr2:238069324:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.15"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SCN1A","chr2:165991531","SCN1A(E1915V)",null,null,"topological domain (Cytoplasmic ), domain (IQ ), sequence variant (In EIEE6. ), sequence variant (In EIEE6. )","domain:IQ","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Generalized epilepsy with febrile seizures plus 2 (GEFS+2) [MIM:604403]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269|PubMed:10742094, ECO:0000269|PubMed:11254444, ECO:0000269|PubMed:11254445, ECO:0000269|PubMed:11524484, ECO:0000269|PubMed:11756608, ECO:0000269|PubMed:12535936, ECO:0000269|PubMed:12576172, ECO:0000269|PubMed:12919402, ECO:0000269|PubMed:14672992, ECO:0000269|PubMed:15525788, ECO:0000269|PubMed:15694566, ECO:0000269|PubMed:15715999, ECO:0000269|PubMed:16525050, ECO:0000269|PubMed:17347258, ECO:0000269|PubMed:17507202, ECO:0000269|PubMed:17561957, ECO:0000269|PubMed:17927801, ECO:0000269|PubMed:17928445, ECO:0000269|PubMed:18251839, ECO:0000269|PubMed:18413471, ECO:0000269|PubMed:18566737, ECO:0000269|PubMed:19339291, ECO:0000269|PubMed:19464195, ECO:0000269|PubMed:19522081, ECO:0000269|PubMed:20117752, ECO:0000269|PubMed:20550552, ECO:0000269|PubMed:20600615, ECO:0000269|PubMed:20729507, ECO:0000269|PubMed:21248271, ECO:0000269|PubMed:21864321}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 6 (EIEE6) [MIM:607208]: A severe form of epileptic encephalopathy characterized by generalized tonic, clonic, and tonic-clonic seizures that are initially induced by fever and begin during the first year of life. Later, patients also manifest other seizure types, including absence, myoclonic, and simple and complex partial seizures. Psychomotor development delay is observed around the second year of life. Some patients manifest a borderline disease phenotype and do not necessarily fulfill all diagnostic criteria for core EIEE6. EIEE6 is considered to be the most severe phenotype within the spectrum of generalized epilepsies with febrile seizures-plus. {ECO:0000269|PubMed:11359211, ECO:0000269|PubMed:12083760, ECO:0000269|PubMed:12566275, ECO:0000269|PubMed:12754708, ECO:0000269|PubMed:12821740, ECO:0000269|PubMed:14504318, ECO:0000269|PubMed:14672992, ECO:0000269|PubMed:14738421, ECO:0000269|PubMed:15087100, ECO:0000269|PubMed:15944908, ECO:0000269|PubMed:16122630, ECO:0000269|PubMed:16458823, ECO:0000269|PubMed:16713920, ECO:0000269|PubMed:17054684, ECO:0000269|PubMed:17054685, ECO:0000269|PubMed:17129991, ECO:0000269|PubMed:17347258, ECO:0000269|PubMed:17561957, ECO:0000269|PubMed:18413471, ECO:0000269|PubMed:18639757, ECO:0000269|PubMed:18930999, ECO:0000269|PubMed:19522081, ECO:0000269|PubMed:19563458, ECO:0000269|PubMed:19589774, ECO:0000269|PubMed:19783390, ECO:0000269|PubMed:20110217, ECO:0000269|PubMed:20431604, ECO:0000269|PubMed:20452746, ECO:0000269|PubMed:20522430, ECO:0000269|PubMed:20729507, ECO:0000269|PubMed:21248271, ECO:0000269|PubMed:21864321, ECO:0000269|PubMed:22092154, ECO:0000269|PubMed:22612257, ECO:0000269|PubMed:23195492, ECO:0000269|PubMed:23662938, ECO:0000269|PubMed:23708187, ECO:0000269|PubMed:25818041, ECO:0000269|PubMed:26993267, ECO:0000269|PubMed:27864847, ECO:0000269|PubMed:28544625}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Intractable childhood epilepsy with generalized tonic- clonic seizures (ICEGTC) [MIM:607208]: A disorder characterized by generalized tonic-clonic seizures beginning usually in infancy and induced by fever. Seizures are associated with subsequent mental decline, as well as ataxia or hypotonia. ICEGTC is similar to SMEI, except for the absence of myoclonic seizures. {ECO:0000269|PubMed:12566275, ECO:0000269|PubMed:16210358, ECO:0000269|PubMed:17507202, ECO:0000269|PubMed:23195492, ECO:0000269|PubMed:23708187}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Migraine, familial hemiplegic, 3 (FHM3) [MIM:609634]: A subtype of migraine associated with transient blindness in some families. Migraine is a disabling symptom complex of periodic headaches, usually temporal and unilateral. Headaches are often accompanied by irritability, nausea, vomiting and photophobia, preceded by constriction of the cranial arteries. The two major subtypes are common migraine (migraine without aura) and classic migraine (migraine with aura). Classic migraine is characterized by recurrent attacks of reversible neurological symptoms (aura) that precede or accompany the headache. Aura may include a combination of sensory disturbances, such as blurred vision, hallucinations, vertigo, numbness and difficulty in concentrating and speaking. {ECO:0000269|PubMed:16054936, ECO:0000269|PubMed:17397047, ECO:0000269|PubMed:18021921, ECO:0000269|PubMed:19332696}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Febrile seizures, familial, 3A (FEB3A) [MIM:604403]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269|PubMed:16326807, ECO:0000269|PubMed:19522081}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=SCN1A mutations may be involved in Panayiotopoulos syndrome, a benign age-related focal seizure disorder occurring in early and mid-childhood. It is characterized by seizures, often prolonged, with predominantly autonomic symptoms, and by an electroencephalogram that shows shifting and/or multiple foci, often with occipital predominance. Autonomic seizures in Panayiotopoulos syndrome consist of episodes of disturbed autonomic function with emesis as the predominant symptom. Cardiorespiratory arrest is exceptional. {ECO:0000269|PubMed:17679682, ECO:0000269|PubMed:19339291, ECO:0000269|PubMed:19522081}.; ","FUNCTION: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in somatosensory neurons induces pain without neurogenic inflammation and produces hypersensitivity to mechanical, but not thermal stimuli. {ECO:0000250|UniProtKB:A2APX8}.; ","epilepsy",{"$nulls":3},"p.Glu1915Val","c.5744A>T","MODERATE","1915/2009",28,{"$nulls":5},"5","602","558","453","417","528","488","0","0","0","0.0553",{"$nulls":20},"4.14658",".;.;.;-4.22;.;-4.22;.;-4.17;-4.15",".;.;.;3.93;.;3.93;.;.;.","1",".;.;.;-6.44;.;-6.44;.;-6.44;-6.44",".;.;.;.;1.0;.;1.0;1.0;.",".;.;.;0.0;.;0.0;.;0.0;0.0",".;.;.;0.588;.;0.643;.;0.684;0.78",{"$nulls":3},"Unknown",-1,"AD","Migraine, familial hemiplegic 3","Neurologic",{"$nulls":3},"C1858673| C1864987| C4551549","0/0","587,0","0","587","0/1","507,30","0.0559","537",null,"chr2:165991531:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.06"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SCN1A","chr2:165991531","SCN1A(E1915V)",null,null,"topological domain (Cytoplasmic ), domain (IQ ), sequence variant (In EIEE6. ), sequence variant (In EIEE6. )","domain:IQ","LOW",null,255,"PASS","Missense",null,-1,"DISEASE: Generalized epilepsy with febrile seizures plus 2 (GEFS+2) [MIM:604403]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269|PubMed:10742094, ECO:0000269|PubMed:11254444, ECO:0000269|PubMed:11254445, ECO:0000269|PubMed:11524484, ECO:0000269|PubMed:11756608, ECO:0000269|PubMed:12535936, ECO:0000269|PubMed:12576172, ECO:0000269|PubMed:12919402, ECO:0000269|PubMed:14672992, ECO:0000269|PubMed:15525788, ECO:0000269|PubMed:15694566, ECO:0000269|PubMed:15715999, ECO:0000269|PubMed:16525050, ECO:0000269|PubMed:17347258, ECO:0000269|PubMed:17507202, ECO:0000269|PubMed:17561957, ECO:0000269|PubMed:17927801, ECO:0000269|PubMed:17928445, ECO:0000269|PubMed:18251839, ECO:0000269|PubMed:18413471, ECO:0000269|PubMed:18566737, ECO:0000269|PubMed:19339291, ECO:0000269|PubMed:19464195, ECO:0000269|PubMed:19522081, ECO:0000269|PubMed:20117752, ECO:0000269|PubMed:20550552, ECO:0000269|PubMed:20600615, ECO:0000269|PubMed:20729507, ECO:0000269|PubMed:21248271, ECO:0000269|PubMed:21864321}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epileptic encephalopathy, early infantile, 6 (EIEE6) [MIM:607208]: A severe form of epileptic encephalopathy characterized by generalized tonic, clonic, and tonic-clonic seizures that are initially induced by fever and begin during the first year of life. Later, patients also manifest other seizure types, including absence, myoclonic, and simple and complex partial seizures. Psychomotor development delay is observed around the second year of life. Some patients manifest a borderline disease phenotype and do not necessarily fulfill all diagnostic criteria for core EIEE6. EIEE6 is considered to be the most severe phenotype within the spectrum of generalized epilepsies with febrile seizures-plus. {ECO:0000269|PubMed:11359211, ECO:0000269|PubMed:12083760, ECO:0000269|PubMed:12566275, ECO:0000269|PubMed:12754708, ECO:0000269|PubMed:12821740, ECO:0000269|PubMed:14504318, ECO:0000269|PubMed:14672992, ECO:0000269|PubMed:14738421, ECO:0000269|PubMed:15087100, ECO:0000269|PubMed:15944908, ECO:0000269|PubMed:16122630, ECO:0000269|PubMed:16458823, ECO:0000269|PubMed:16713920, ECO:0000269|PubMed:17054684, ECO:0000269|PubMed:17054685, ECO:0000269|PubMed:17129991, ECO:0000269|PubMed:17347258, ECO:0000269|PubMed:17561957, ECO:0000269|PubMed:18413471, ECO:0000269|PubMed:18639757, ECO:0000269|PubMed:18930999, ECO:0000269|PubMed:19522081, ECO:0000269|PubMed:19563458, ECO:0000269|PubMed:19589774, ECO:0000269|PubMed:19783390, ECO:0000269|PubMed:20110217, ECO:0000269|PubMed:20431604, ECO:0000269|PubMed:20452746, ECO:0000269|PubMed:20522430, ECO:0000269|PubMed:20729507, ECO:0000269|PubMed:21248271, ECO:0000269|PubMed:21864321, ECO:0000269|PubMed:22092154, ECO:0000269|PubMed:22612257, ECO:0000269|PubMed:23195492, ECO:0000269|PubMed:23662938, ECO:0000269|PubMed:23708187, ECO:0000269|PubMed:25818041, ECO:0000269|PubMed:26993267, ECO:0000269|PubMed:27864847, ECO:0000269|PubMed:28544625}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Intractable childhood epilepsy with generalized tonic- clonic seizures (ICEGTC) [MIM:607208]: A disorder characterized by generalized tonic-clonic seizures beginning usually in infancy and induced by fever. Seizures are associated with subsequent mental decline, as well as ataxia or hypotonia. ICEGTC is similar to SMEI, except for the absence of myoclonic seizures. {ECO:0000269|PubMed:12566275, ECO:0000269|PubMed:16210358, ECO:0000269|PubMed:17507202, ECO:0000269|PubMed:23195492, ECO:0000269|PubMed:23708187}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Migraine, familial hemiplegic, 3 (FHM3) [MIM:609634]: A subtype of migraine associated with transient blindness in some families. Migraine is a disabling symptom complex of periodic headaches, usually temporal and unilateral. Headaches are often accompanied by irritability, nausea, vomiting and photophobia, preceded by constriction of the cranial arteries. The two major subtypes are common migraine (migraine without aura) and classic migraine (migraine with aura). Classic migraine is characterized by recurrent attacks of reversible neurological symptoms (aura) that precede or accompany the headache. Aura may include a combination of sensory disturbances, such as blurred vision, hallucinations, vertigo, numbness and difficulty in concentrating and speaking. {ECO:0000269|PubMed:16054936, ECO:0000269|PubMed:17397047, ECO:0000269|PubMed:18021921, ECO:0000269|PubMed:19332696}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Febrile seizures, familial, 3A (FEB3A) [MIM:604403]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269|PubMed:16326807, ECO:0000269|PubMed:19522081}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=SCN1A mutations may be involved in Panayiotopoulos syndrome, a benign age-related focal seizure disorder occurring in early and mid-childhood. It is characterized by seizures, often prolonged, with predominantly autonomic symptoms, and by an electroencephalogram that shows shifting and/or multiple foci, often with occipital predominance. Autonomic seizures in Panayiotopoulos syndrome consist of episodes of disturbed autonomic function with emesis as the predominant symptom. Cardiorespiratory arrest is exceptional. {ECO:0000269|PubMed:17679682, ECO:0000269|PubMed:19339291, ECO:0000269|PubMed:19522081}.; ","FUNCTION: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in somatosensory neurons induces pain without neurogenic inflammation and produces hypersensitivity to mechanical, but not thermal stimuli. {ECO:0000250|UniProtKB:A2APX8}.; ","epilepsy",{"$nulls":3},"p.Glu1915Val","c.5744A>T","MODERATE","1915/2009",28,{"$nulls":5},"5","602","485","453","364","527","434","0","0","0","0.1221",{"$nulls":20},"4.14658",".;.;.;-4.22;.;-4.22;.;-4.17;-4.15",".;.;.;3.93;.;3.93;.;.;.","1",".;.;.;-6.44;.;-6.44;.;-6.44;-6.44",".;.;.;.;1.0;.;1.0;1.0;.",".;.;.;0.0;.;0.0;.;0.0;0.0",".;.;.;0.588;.;0.643;.;0.684;0.78",{"$nulls":3},"Unknown",-1,"AD","Migraine, familial hemiplegic 3","Neurologic",{"$nulls":3},"C1858673| C1864987| C4551549","0/0","588,0","0","588","0/1","417,59","0.1239","476",null,"chr2:165991531:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1209"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SELT","chr3:150624873","SELT(T146I)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Thr146Ile","c.437C>T","MODERATE","146/195",4,{"$nulls":5},"5","482","434","330","281","435","372","0","0","0","0.0565",{"$nulls":20},"4.151516","0.89;.;0.89;0.89;0.89",".;.;2.455;.;.","1","-4.8;.;-5.0;-4.8;-4.8",".;.;1.0;.;.","0.001;.;0.002;0.001;0.001","0.979;0.984;.;0.979;0.979",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","467,0","0","467","0/1","399,26","0.0612","425",null,"chr3:150624873:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0641"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SEMA5A","chr5:9379897","SEMA5A(W17*)",null,null,"signal peptide ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Bifunctional axonal guidance cue regulated by sulfated proteoglycans; attractive effects result from interactions with heparan sulfate proteoglycans (HSPGs), while the inhibitory effects depend on interactions with chondroitin sulfate proteoglycans (CSPGs) (By similarity). Ligand for receptor PLXNB3. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1. May promote angiogenesis by increasing endothelial cell proliferation and migration and inhibiting apoptosis. {ECO:0000250, ECO:0000269|PubMed:15218527, ECO:0000269|PubMed:19850054, ECO:0000269|PubMed:20696765, ECO:0000269|PubMed:21706053}.; ",{"$nulls":4},"p.Trp17*","c.50G>A","HIGH","17/1074",3,{"$nulls":5},"5","764","573","521","374","716","531","0","0","0","0.0546",{"$nulls":5},"(SEMA5A|ENSG00000112902|1|1.00)","(SEMA5A|ENSG00000112902|1|1.00)",{"$nulls":13},"5.631895",null,null,"1",{"$nulls":3},"0.664;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","751,0","0","751","0/1","513,34","0.0622","547",null,"chr5:9379897:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0722"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SEMA6C","chr1:151132747","SEMA6C(L876M)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections. {ECO:0000269|PubMed:12110693}.; ",{"$nulls":4},"p.Leu876Met","c.2626C>A","MODERATE","876/962",20,{"$nulls":5},"5","137","109","109","92","123","96","0","0","0","0.0938",{"$nulls":20},"2.450293","2.02;2.21;2.03;2.03",".;.;0.695;0.695","1","0.05;0.05;0.06;0.06","0.999;0.999;0.998;0.998","0.443;0.446;0.471;0.471","0.24;0.244;0.18;0.182",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","137,0","0","137","0/1","95,12","0.1121","107",null,"chr1:151132747:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1087"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SETD1A","chr16:30979948","SETD1A(A1388T)",{"$nulls":6},255,"PASS","Missense","rs552578757",0.006134969325153374,null,"FUNCTION: Histone methyltransferase that specifically methylates 'Lys-4' of histone H3, when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys- 9' residue is already methylated. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. The non-overlapping localization with SETD1B suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. {ECO:0000269|PubMed:12670868}.; ",{"$nulls":4},"p.Ala1388Thr","c.4162G>A","MODERATE","1388/1707",14,{"$nulls":5},"5","100","70","73","51","88","50","0","0","0","0.18",{"$nulls":20},"2.832856","0.34","0.805","1","-0.27","0.99","0.002","0.458",{"$nulls":3},"1000Gp3_SAS_AF",0.006134969325153374,{"$nulls":4},"SET1A is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. The complex is the analog of the S. cerevisiae Set1/COMPASS complex (Lee and Skalnik, 2005 [PubMed 16253997]). Also see SET1B (MIM 611055).[supplied by OMIM, Mar 2008].  ",null,"CN272918","0/0","99,0","0","99","0/1","55,12","0.1791","67",null,"chr16:30979948:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1569"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SETD1A","chr16:30979948","SETD1A(A1388T)",{"$nulls":6},255,"PASS","Missense","rs552578757",0.006134969325153374,null,"FUNCTION: Histone methyltransferase that specifically methylates 'Lys-4' of histone H3, when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys- 9' residue is already methylated. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. The non-overlapping localization with SETD1B suggests that SETD1A and SETD1B make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. {ECO:0000269|PubMed:12670868}.; ",{"$nulls":4},"p.Ala1388Thr","c.4162G>A","MODERATE","1388/1707",14,{"$nulls":5},"4","100","67","73","46",null,null,"0","0",{"$nulls":22},"2.832856","0.34","0.805","1","-0.27","0.99","0.002","0.458",{"$nulls":3},"1000Gp3_SAS_AF",0.006134969325153374,{"$nulls":4},"SET1A is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. The complex is the analog of the S. cerevisiae Set1/COMPASS complex (Lee and Skalnik, 2005 [PubMed 16253997]). Also see SET1B (MIM 611055).[supplied by OMIM, Mar 2008].  ",null,"CN272918","0/0","82,0","0","82","0/1","45,5","0.1","50",null,"chr16:30979948:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1087"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SLC35G3","chr17:35193740","SLC35G3(A190T)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense","rs201078434",7.5642965204236008E-4,{"$nulls":6},"p.Ala190Thr","c.568G>A","MODERATE","190/338",1,1,{"$nulls":4},"5","561","328","459","264","479","278","0.0018","0.0018","0","0.0791",{"$nulls":20},"0.611457","1.44","0.345","0.861711","-0.74","0.004","0.096","0.045",{"$nulls":3},"1000Gp3_AFR_AF",7.5642965204236008E-4,{"$nulls":7},"0/0","556,1","0.0018","557","0/1","298,25","0.0774","323",null,"chr17:35193740:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0758"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SLC9C1","chr3:112168924","SLC9C1(R1064*)",{"$nulls":6},255,"PASS","Loss Of Function","rs202229232",0.000992063492063492,null,"FUNCTION: Sperm-specific sodium/hydrogen exchanger involved in intracellular pH regulation of spermatozoa. Required for sperm motility and fertility. Involved in sperm cell hyperactivation, a step needed for sperm motility which is essential late in the preparation of sperm for fertilization. Required for the expression and bicarbonate regulation of the soluble adenylyl cyclase (sAC) (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg1064*","c.3190C>T","HIGH","1064/1177",25,3,{"$nulls":4},"4","222","172","164","122","197","145","0","0","0","0.0621",{"$nulls":5},"(SLC9C1|ENSG00000172139|1|1.00)","(SLC9C1|ENSG00000172139|1|1.00)",{"$nulls":13},"7.401726",null,null,"1",{"$nulls":3},"0.291;0.318",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":4},"SLC9A10 is a member of the sodium-hydrogen exchanger (NHE) family (see SLC9A1, MIM 107310) and is required for male fertility and sperm motility (Wang et al., 2003 [PubMed 14634667]).[supplied by OMIM, Apr 2009].  ",null,null,"0/0","221,0","0","221","0/1","162,9","0.0526","171",null,"chr3:112168924:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0656"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SLC9C1","chr3:112168924","SLC9C1(R1064*)",{"$nulls":6},255,"PASS","Loss Of Function","rs202229232",0.000992063492063492,null,"FUNCTION: Sperm-specific sodium/hydrogen exchanger involved in intracellular pH regulation of spermatozoa. Required for sperm motility and fertility. Involved in sperm cell hyperactivation, a step needed for sperm motility which is essential late in the preparation of sperm for fertilization. Required for the expression and bicarbonate regulation of the soluble adenylyl cyclase (sAC) (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg1064*","c.3190C>T","HIGH","1064/1177",25,3,{"$nulls":4},"5","222","168","164","131","199","152","0","0","0","0.0789",{"$nulls":5},"(SLC9C1|ENSG00000172139|1|1.00)","(SLC9C1|ENSG00000172139|1|1.00)",{"$nulls":13},"7.401726",null,null,"1",{"$nulls":3},"0.291;0.318",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":4},"SLC9A10 is a member of the sodium-hydrogen exchanger (NHE) family (see SLC9A1, MIM 107310) and is required for male fertility and sperm motility (Wang et al., 2003 [PubMed 14634667]).[supplied by OMIM, Apr 2009].  ",null,null,"0/0","221,0","0","221","0/1","155,13","0.0774","168",null,"chr3:112168924:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0763"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SMPD4","chr2:130156134","SMPD4(V436fs)",null,null,"splice variant (In isoform 5. ), sequence variant (In NEDMABA. ), sequence variant (In NEDMABA. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (PubMed:16517606). May sensitize cells to DNA damage-induced apoptosis (PubMed:18505924). {ECO:0000269|PubMed:16517606, ECO:0000269|PubMed:18505924}.; ",{"$nulls":4},"p.Val436fs","c.1306-55_1306delCCACCGAGTATTTGGCCCCCAGCCACGGAGCCCTTAGCACACACCTCCCCCACAGG","HIGH","436/866",14,{"$nulls":20},"130156190",{"$nulls":26},"Unknown",-1,{"$nulls":6},"C5231431",{"$nulls":9},"chr2:130156134:ACCTGTGGGGGAGGTGTGTGCTAAGGGCTCCGTGGCTGGGGGCCAAATACTCGGTGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SMPD4","chr2:130156134","SMPD4(V436fs)",null,null,"splice variant (In isoform 5. ), sequence variant (In NEDMABA. ), sequence variant (In NEDMABA. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (PubMed:16517606). May sensitize cells to DNA damage-induced apoptosis (PubMed:18505924). {ECO:0000269|PubMed:16517606, ECO:0000269|PubMed:18505924}.; ",{"$nulls":4},"p.Val436fs","c.1306-55_1306delCCACCGAGTATTTGGCCCCCAGCCACGGAGCCCTTAGCACACACCTCCCCCACAGG","HIGH","436/866",14,{"$nulls":5},"3",null,null,"217","146","139","98",null,null,"0","0.102",{"$nulls":5},"(SMPD4|ENSG00000136699|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":6},"C5231431","0/0","350,0","0","350","0/1","226,13","0.0544","239",null,"chr2:130156134:ACCTGTGGGGGAGGTGTGTGCTAAGGGCTCCGTGGCTGGGGGCCAAATACTCGGTGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1096"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SMPD4","chr2:130156134","SMPD4(V436fs)",null,null,"splice variant (In isoform 5. ), sequence variant (In NEDMABA. ), sequence variant (In NEDMABA. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide (PubMed:16517606). May sensitize cells to DNA damage-induced apoptosis (PubMed:18505924). {ECO:0000269|PubMed:16517606, ECO:0000269|PubMed:18505924}.; ",{"$nulls":4},"p.Val436fs","c.1306-55_1306delCCACCGAGTATTTGGCCCCCAGCCACGGAGCCCTTAGCACACACCTCCCCCACAGG","HIGH","436/866",14,{"$nulls":5},"3",null,null,"217","116","139","80",null,null,"0","0.1625",{"$nulls":5},"(SMPD4|ENSG00000136699|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":6},"C5231431","0/0","350,0","0","350","0/1","166,15","0.0829","181",null,"chr2:130156134:ACCTGTGGGGGAGGTGTGTGCTAAGGGCTCCGTGGCTGGGGGCCAAATACTCGGTGG:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1293"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SON","chr21:33546259","SON(E42K)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: ZTTK syndrome (ZTTKS) [MIM:617140]: An autosomal dominant syndrome characterized by intellectual disability, developmental delay, malformations of the cerebral cortex, epilepsy, vision problems, musculo-skeletal abnormalities, and congenital malformations. {ECO:0000269|PubMed:25590979, ECO:0000269|PubMed:27256762, ECO:0000269|PubMed:27545676, ECO:0000269|PubMed:27545680}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: RNA-binding protein that acts as a mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. Specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Probably acts by facilitating the interaction between Serine/arginine-rich proteins such as SRSF2 and the RNA polymerase II. Also binds to DNA; binds to the consensus DNA sequence: 5'- GA[GT]AN[CG][AG]CC-3'. May indirectly repress hepatitis B virus (HBV) core promoter activity and transcription of HBV genes and production of HBV virions. Essential for correct RNA splicing of multiple genes critical for brain development, neuronal migration and metabolism, including TUBG1, FLNA, PNKP, WDR62, PSMD3, PCK2, PFKL, IDH2, and ACY1 (PubMed:27545680). {ECO:0000269|PubMed:20581448, ECO:0000269|PubMed:21504830, ECO:0000269|PubMed:27545680}.; ",{"$nulls":4},"p.Glu42Lys","c.124G>A","MODERATE","42/2426",2,{"$nulls":5},"5","112","68","88","53","99","54","0","0","0","0.1481",{"$nulls":20},"4.172576","2.34","0.895;.;0.895;0.895","0.841058;0.996727;0.841058;0.870181;0.841058","-1.37;0.96;-1.51;-1.69","0.997;.;0.997;0.997","0.002;0.0;0.003;0.004","0.684;0.337;0.658;0.632",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4310696","0/0","112,0","0","112","0/1","53,12","0.1846","65",null,"chr21:33546259:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.1509"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SPIRE2","chr16:89859165","SPIRE2(E425K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as an actin nucleation factor, remains associated with the slow-growing pointed end of the new filament (PubMed:21620703). Involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport (By similarity). Required for asymmetric spindle positioning and asymmetric cell division during meiosis (PubMed:21620703). Required for normal formation of the cleavage furrow and for polar body extrusion during female germ cell meiosis (PubMed:21620703). Also acts in the nucleus: together with SPIRE1 and SPIRE2, promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage (PubMed:26287480). {ECO:0000250|UniProtKB:Q8K1S6, ECO:0000269|PubMed:21620703, ECO:0000269|PubMed:26287480}.; ",{"$nulls":4},"p.Glu425Lys","c.1273G>A","MODERATE","425/714",9,{"$nulls":5},"5","494","466","415","387","419","361","0","0","0","0.0609",{"$nulls":20},"5.6958459999999995","0.79","2.6","1","-2.32;-2.25","0.993","0.007;0.006","0.519;0.53",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","479,0","0","479","0/1","423,27","0.06","450",null,"chr16:89859165:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0594"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SPIRE2","chr16:89859165","SPIRE2(E425K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as an actin nucleation factor, remains associated with the slow-growing pointed end of the new filament (PubMed:21620703). Involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport (By similarity). Required for asymmetric spindle positioning and asymmetric cell division during meiosis (PubMed:21620703). Required for normal formation of the cleavage furrow and for polar body extrusion during female germ cell meiosis (PubMed:21620703). Also acts in the nucleus: together with SPIRE1 and SPIRE2, promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage (PubMed:26287480). {ECO:0000250|UniProtKB:Q8K1S6, ECO:0000269|PubMed:21620703, ECO:0000269|PubMed:26287480}.; ",{"$nulls":4},"p.Glu425Lys","c.1273G>A","MODERATE","425/714",9,{"$nulls":5},"5","494","364","415","300","414","297","0","0","0","0.0909",{"$nulls":20},"5.6958459999999995","0.79","2.6","1","-2.32;-2.25","0.993","0.007;0.006","0.519;0.53",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","480,0","0","480","0/1","323,30","0.085","353",null,"chr16:89859165:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.09"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SREBF1","chr17:17816249","SREBF1(L754F)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform SREBP-1aDelta and isoform SREBP-1cDelta. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator required for lipid homeostasis. Regulates transcription of the LDL receptor gene as well as the fatty acid and to a lesser degree the cholesterol synthesis pathway (By similarity). Binds to the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3'). Has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3'). {ECO:0000250|UniProtKB:Q9WTN3}.; ",{"$nulls":4},"p.Leu754Phe","c.2262G>C","MODERATE","754/1177",12,{"$nulls":5},"5","424","322","364","259","336","254","0","0","0","0.0787",{"$nulls":20},"2.377149","2.53",".;.;2.37","0.999991;0.999988;0.999988;0.999988","-2.87",".;1.0;0.999","0.006;0.005;0.006","0.718;0.707;0.677",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","354,0","0","354","0/1","243,25","0.0933","268",null,"chr17:17816249:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0811"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SREBF1","chr17:17816249","SREBF1(L754F)",null,null,"topological domain (Cytoplasmic ), splice variant (In isoform SREBP-1aDelta and isoform SREBP-1cDelta. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcriptional activator required for lipid homeostasis. Regulates transcription of the LDL receptor gene as well as the fatty acid and to a lesser degree the cholesterol synthesis pathway (By similarity). Binds to the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3'). Has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3'). {ECO:0000250|UniProtKB:Q9WTN3}.; ",{"$nulls":4},"p.Leu754Phe","c.2262G>C","MODERATE","754/1177",12,{"$nulls":5},"5","424","262","364","204","339","215","0","0","0","0.1163",{"$nulls":20},"2.377149","2.53",".;.;2.37","0.999991;0.999988;0.999988;0.999988","-2.87",".;1.0;0.999","0.006;0.005;0.006","0.718;0.707;0.677",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","350,0","0","350","0/1","193,24","0.1106","217",null,"chr17:17816249:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1127"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","STARD9","chr15:42693631","STARD9(P4018Q)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Microtubule-dependent motor protein required for spindle pole assembly during mitosis. Required to stabilize the pericentriolar material (PCM). {ECO:0000269|PubMed:22153075}.; ",{"$nulls":4},"p.Pro4018Gln","c.12053C>A","MODERATE","4018/4700",23,{"$nulls":5},"5","1027","866","802","654","871","752","0.001","0.001","0","0.137",{"$nulls":20},"1.411246","-0.15","1.895","1","-2.15",null,null,"0.218",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1005,0","0","1005","0/1","717,118","0.1413","835",null,"chr15:42693631:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1422"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","STARD9","chr15:42693631","STARD9(P4018Q)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Microtubule-dependent motor protein required for spindle pole assembly during mitosis. Required to stabilize the pericentriolar material (PCM). {ECO:0000269|PubMed:22153075}.; ",{"$nulls":4},"p.Pro4018Gln","c.12053C>A","MODERATE","4018/4700",23,{"$nulls":5},"5","1027","725","802","557","874","623","0.001","0.001","0","0.1766",{"$nulls":20},"1.411246","-0.15","1.895","1","-2.15",null,null,"0.218",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1010,0","0","1010","0/1","576,121","0.1736","697",null,"chr15:42693631:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1777"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","STK3","chr8:98749276","STK3(Sequence Feature)",{"$nulls":3},"modified-residue:Phosphothreonine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,null,"FUNCTION: Stress-activated, pro-apoptotic kinase which, following caspase-cleavage, enters the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation. Key component of the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Phosphorylation of YAP1 by LATS2 inhibits its translocation into the nucleus to regulate cellular genes important for cell proliferation, cell death, and cell migration. STK3/MST2 and STK4/MST1 are required to repress proliferation of mature hepatocytes, to prevent activation of facultative adult liver stem cells (oval cells), and to inhibit tumor formation. Phosphorylates NKX2-1 (By similarity). Phosphorylates NEK2 and plays a role in centrosome disjunction by regulating the localization of NEK2 to centrosome, and its ability to phosphorylate CROCC and CEP250. In conjunction with SAV1, activates the transcriptional activity of ESR1 through the modulation of its phosphorylation. Positively regulates RAF1 activation via suppression of the inhibitory phosphorylation of RAF1 on 'Ser-259'. Phosphorylates MOBKL1A and RASSF2. Phosphorylates MOBKL1B on 'Thr-74'. Acts cooperatively with MOBKL1B to activate STK38. {ECO:0000250|UniProtKB:Q9JI10, ECO:0000269|PubMed:15688006, ECO:0000269|PubMed:16930133, ECO:0000269|PubMed:18328708, ECO:0000269|PubMed:18362890, ECO:0000269|PubMed:19525978, ECO:0000269|PubMed:20212043, ECO:0000269|PubMed:21076410, ECO:0000269|PubMed:21104395, ECO:0000269|PubMed:28087714, ECO:0000269|PubMed:8566796, ECO:0000269|PubMed:8816758}.; ","level2",{"$nulls":4},"c.435A>C","MODERATE",null,6,{"$nulls":5},"5","285","337","229","260","215","242","0","0","0","0.0744",{"$nulls":31},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","282,0","0","282","0/1","300,22","0.0683","322",null,"chr8:98749276:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0654"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","STK3","chr8:98749276","STK3(Sequence Feature)",{"$nulls":3},"modified-residue:Phosphothreonine","MODERATE",null,255,"PASS","Sequence Feature",null,-1,null,"FUNCTION: Stress-activated, pro-apoptotic kinase which, following caspase-cleavage, enters the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation. Key component of the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Phosphorylation of YAP1 by LATS2 inhibits its translocation into the nucleus to regulate cellular genes important for cell proliferation, cell death, and cell migration. STK3/MST2 and STK4/MST1 are required to repress proliferation of mature hepatocytes, to prevent activation of facultative adult liver stem cells (oval cells), and to inhibit tumor formation. Phosphorylates NKX2-1 (By similarity). Phosphorylates NEK2 and plays a role in centrosome disjunction by regulating the localization of NEK2 to centrosome, and its ability to phosphorylate CROCC and CEP250. In conjunction with SAV1, activates the transcriptional activity of ESR1 through the modulation of its phosphorylation. Positively regulates RAF1 activation via suppression of the inhibitory phosphorylation of RAF1 on 'Ser-259'. Phosphorylates MOBKL1A and RASSF2. Phosphorylates MOBKL1B on 'Thr-74'. Acts cooperatively with MOBKL1B to activate STK38. {ECO:0000250|UniProtKB:Q9JI10, ECO:0000269|PubMed:15688006, ECO:0000269|PubMed:16930133, ECO:0000269|PubMed:18328708, ECO:0000269|PubMed:18362890, ECO:0000269|PubMed:19525978, ECO:0000269|PubMed:20212043, ECO:0000269|PubMed:21076410, ECO:0000269|PubMed:21104395, ECO:0000269|PubMed:28087714, ECO:0000269|PubMed:8566796, ECO:0000269|PubMed:8816758}.; ","level2",{"$nulls":4},"c.435A>C","MODERATE",null,6,{"$nulls":5},"4","285","314",null,null,"216","222","0","0","0","0.0721",{"$nulls":31},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","281,0","0","281","0/1","275,17","0.0582","292",null,"chr8:98749276:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SULT6B1","chr2:37179568","SULT6B1(R140Q)",{"$nulls":3},"binding-site:PAPS","LOW",null,255,"PASS","Missense","rs11569744",0.006128007262823422,null,"FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of thyroxine. Involved in the metabolism of thyroxine (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg140Gln","c.419G>A","MODERATE","140/303",4,5,{"$nulls":4},"5","218","142","139","104","199","124","0","0","0","0.1613",{"$nulls":20},"3.202152","-0.37","4.31;.","0.999846;0.999997;0.999846;1","-3.77;-3.94","1.0;.","0.0","0.432;0.424",{"$nulls":3},"ESP6500_AA_AF",0.006128007262823422,{"$nulls":7},"0/0","215,0","0","215","0/1","118,25","0.1748","143",null,"chr2:37179568:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1635"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SULT6B1","chr2:37179568","SULT6B1(R140Q)",{"$nulls":3},"binding-site:PAPS","LOW",null,255,"PASS","Missense","rs11569744",0.006128007262823422,null,"FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of thyroxine. Involved in the metabolism of thyroxine (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Arg140Gln","c.419G>A","MODERATE","140/303",4,5,{"$nulls":4},"5","218","154","139","102","198","141","0","0","0","0.1844",{"$nulls":20},"3.202152","-0.37","4.31;.","0.999846;0.999997;0.999846;1","-3.77;-3.94","1.0;.","0.0","0.432;0.424",{"$nulls":3},"ESP6500_AA_AF",0.006128007262823422,{"$nulls":7},"0/0","213,0","0","213","0/1","121,29","0.1933","150",null,"chr2:37179568:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1765"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","SYNC","chr1:32695943","SYNC(S52C)",null,null,"region of interest (Head )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Atypical type III intermediate filament (IF) protein that may play a supportive role in the efficient coupling of mechanical stress between the myofibril and fiber exterior. May facilitate lateral force transmission during skeletal muscle contraction. Does not form homofilaments nor heterofilaments with other IF proteins. {ECO:0000250|UniProtKB:Q9EPM5}.; ",{"$nulls":4},"p.Ser52Cys","c.155C>G","MODERATE","52/482",2,{"$nulls":5},"5","684","514","523","391","555","432","0","0","0","0.081",{"$nulls":20},"0.888415","1.67","0.345","1","-0.63;-0.55","0.102;0.415","0.008;0.007","0.127;0.123",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the intermediate filament family which contains an N-terminal head domain, followed by a central coiled-coil region and a short C-terminal tail. The protein is highly expressed in skeletal and cardiac muscle. The protein links the dystrophin associated protein complex (DAPC) to desmin filaments in muscle and may have a structural role in striated muscle. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009].",null,null,"0/0","674,0","0","674","0/1","464,42","0.083","506",null,"chr1:32695943:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0767"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","SYNC","chr1:32695943","SYNC(S52C)",null,null,"region of interest (Head )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Atypical type III intermediate filament (IF) protein that may play a supportive role in the efficient coupling of mechanical stress between the myofibril and fiber exterior. May facilitate lateral force transmission during skeletal muscle contraction. Does not form homofilaments nor heterofilaments with other IF proteins. {ECO:0000250|UniProtKB:Q9EPM5}.; ",{"$nulls":4},"p.Ser52Cys","c.155C>G","MODERATE","52/482",2,{"$nulls":5},"5","684","451","523","343","555","368","0","0","0","0.0897",{"$nulls":20},"0.888415","1.67","0.345","1","-0.63;-0.55","0.102;0.415","0.008;0.007","0.127;0.123",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the intermediate filament family which contains an N-terminal head domain, followed by a central coiled-coil region and a short C-terminal tail. The protein is highly expressed in skeletal and cardiac muscle. The protein links the dystrophin associated protein complex (DAPC) to desmin filaments in muscle and may have a structural role in striated muscle. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009].",null,null,"0/0","678,0","0","678","0/1","396,39","0.0897","435",null,"chr1:32695943:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0904"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","TAF3","chr10:7963975","TAF3(Q155H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.; ",{"$nulls":4},"p.Gln155His","c.465G>T","MODERATE","155/929",3,1,{"$nulls":4},"5","227","213","168","159","197","182","0","0","0","0.2033",{"$nulls":20},"1.942447","2.0","2.005","0.999992","-2.03","1.0","0.002","0.726",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","226,0","0","226","0/1","167,40","0.1932","207",null,"chr10:7963975:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1761"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TAF3","chr10:7963975","TAF3(Q155H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor TFIID is one of the general factors required for accurate and regulated initiation by RNA polymerase II. TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. Required in complex with TBPL2 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process.; ",{"$nulls":4},"p.Gln155His","c.465G>T","MODERATE","155/929",3,1,{"$nulls":4},"5","227","186","168","144","196","163","0","0","0","0.2515",{"$nulls":20},"1.942447","2.0","2.005","0.999992","-2.03","1.0","0.002","0.726",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","226,0","0","226","0/1","131,50","0.2762","181",null,"chr10:7963975:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2431"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","TCF7L2","chr10:113165557","TCF7L2(C486fs)",null,null,"region of interest (Promoter-specific activation domain ), splice variant (In isoform 6. ), splice variant (In isoform 9, isoform 11, isoform 14 and isoform 15. ), splice variant (In isoform 12. ), splice variant (In isoform 2 and isoform 4. ), splice variant (In isoform 10. )",{"$nulls":3},255,"PASS","Loss Of Function","rs769592153",-1,"DISEASE: Note=Constitutive activation and subsequent transactivation of target genes may lead to the maintenance of stem-cell characteristics (cycling and longevity) in cells that should normally undergo terminal differentiation and constitute the primary transforming event in colorectal cancer (CRC).; DISEASE: Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:16415884, ECO:0000269|PubMed:24390345}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Participates in the Wnt signaling pathway and modulates MYC expression by binding to its promoter in a sequence-specific manner. Acts as repressor in the absence of CTNNB1, and as activator in its presence. Activates transcription from promoters with several copies of the Tcf motif 5'-CCTTTGATC-3' in the presence of CTNNB1. TLE1, TLE2, TLE3 and TLE4 repress transactivation mediated by TCF7L2/TCF4 and CTNNB1. Expression of dominant-negative mutants results in cell-cycle arrest in G1. Necessary for the maintenance of the epithelial stem-cell compartment of the small intestine. {ECO:0000269|PubMed:12408868, ECO:0000269|PubMed:12727872, ECO:0000269|PubMed:19443654, ECO:0000269|PubMed:22699938, ECO:0000269|PubMed:9727977}.; ","gedi|level2",{"$nulls":3},"p.Cys486fs","c.1454dupA","HIGH","485/619",15,{"$nulls":5},"4",null,null,"156","144","145","150",null,null,"0","0.16",{"$nulls":5},"(TCF7L2|ENSG00000148737|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"kCANCER,kWNT",null,null,"C0011860","0/0","172,0","0","184","0/1","120,24","0.1667","171",null,"chr10:113165557:G:GA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TCF7L2","chr10:113165557","TCF7L2(C486fs)",null,null,"region of interest (Promoter-specific activation domain ), splice variant (In isoform 6. ), splice variant (In isoform 9, isoform 11, isoform 14 and isoform 15. ), splice variant (In isoform 12. ), splice variant (In isoform 2 and isoform 4. ), splice variant (In isoform 10. )",{"$nulls":3},255,"PASS","Loss Of Function","rs769592153",-1,"DISEASE: Note=Constitutive activation and subsequent transactivation of target genes may lead to the maintenance of stem-cell characteristics (cycling and longevity) in cells that should normally undergo terminal differentiation and constitute the primary transforming event in colorectal cancer (CRC).; DISEASE: Diabetes mellitus, non-insulin-dependent (NIDDM) [MIM:125853]: A multifactorial disorder of glucose homeostasis caused by a lack of sensitivity to the body's own insulin. Affected individuals usually have an obese body habitus and manifestations of a metabolic syndrome characterized by diabetes, insulin resistance, hypertension and hypertriglyceridemia. The disease results in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:16415884, ECO:0000269|PubMed:24390345}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Participates in the Wnt signaling pathway and modulates MYC expression by binding to its promoter in a sequence-specific manner. Acts as repressor in the absence of CTNNB1, and as activator in its presence. Activates transcription from promoters with several copies of the Tcf motif 5'-CCTTTGATC-3' in the presence of CTNNB1. TLE1, TLE2, TLE3 and TLE4 repress transactivation mediated by TCF7L2/TCF4 and CTNNB1. Expression of dominant-negative mutants results in cell-cycle arrest in G1. Necessary for the maintenance of the epithelial stem-cell compartment of the small intestine. {ECO:0000269|PubMed:12408868, ECO:0000269|PubMed:12727872, ECO:0000269|PubMed:19443654, ECO:0000269|PubMed:22699938, ECO:0000269|PubMed:9727977}.; ","gedi|level2",{"$nulls":3},"p.Cys486fs","c.1454dupA","HIGH","485/619",15,{"$nulls":5},"4",null,null,"156","121","145","133",null,null,"0","0.2406",{"$nulls":5},"(TCF7L2|ENSG00000148737|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"kCANCER,kWNT",null,null,"C0011860","0/0","172,0","0","184","0/1","90,37","0.2913","149",null,"chr10:113165557:G:GA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.281"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","TENM4","chr11:78722738","TENM4(D1240fs)",null,null,"topological domain (Extracellular ), repeat (NHL 1 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Tremor, hereditary essential 5 (ETM5) [MIM:616736]: A common movement disorder mainly characterized by postural tremor of the arms. Head, legs, trunk, voice, jaw, and facial muscles also may be involved. The condition can be aggravated by emotions, hunger, fatigue and temperature extremes, and may cause a functional disability or even incapacitation. Inheritance is autosomal dominant. {ECO:0000269|PubMed:26188006}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. Plays a role in the establishment of the anterior-posterior axis during gastrulation. Regulates the differentiation and cellular process formation of oligodendrocytes and myelination of small- diameter axons in the central nervous system (CNS) (PubMed:26188006). Promotes activation of focal adhesion kinase. May function as a cellular signal transducer (By similarity). {ECO:0000250|UniProtKB:Q3UHK6, ECO:0000269|PubMed:26188006}.; ",{"$nulls":4},"p.Asp1240fs","c.3719_3730del>GAN_EAELED<insT","HIGH","1240/2769",24,{"$nulls":20},"78722927",{"$nulls":26},"Unknown",-1,{"$nulls":6},"C4225223",{"$nulls":9},"chr11:78722738:<DELETE_NUC>:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TENM4","chr11:78722738","TENM4(D1240fs)",null,null,"topological domain (Extracellular ), repeat (NHL 1 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Tremor, hereditary essential 5 (ETM5) [MIM:616736]: A common movement disorder mainly characterized by postural tremor of the arms. Head, legs, trunk, voice, jaw, and facial muscles also may be involved. The condition can be aggravated by emotions, hunger, fatigue and temperature extremes, and may cause a functional disability or even incapacitation. Inheritance is autosomal dominant. {ECO:0000269|PubMed:26188006}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. Plays a role in the establishment of the anterior-posterior axis during gastrulation. Regulates the differentiation and cellular process formation of oligodendrocytes and myelination of small- diameter axons in the central nervous system (CNS) (PubMed:26188006). Promotes activation of focal adhesion kinase. May function as a cellular signal transducer (By similarity). {ECO:0000250|UniProtKB:Q3UHK6, ECO:0000269|PubMed:26188006}.; ",{"$nulls":4},"p.Asp1240fs","c.3719_3730del>GAN_EAELED<insT","HIGH","1240/2769",24,{"$nulls":20},"78722927",{"$nulls":26},"Unknown",-1,{"$nulls":6},"C4225223",{"$nulls":9},"chr11:78722738:<DELETE_NUC>:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","THSD7A","chr7:11424729","THSD7A(N1117fs)",null,null,"topological domain (Extracellular ), domain (TSP type-1 14 )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Autoantibodies against THSD7A have been detected in serum and glomeruli from patients with idiopathic membranous nephropathy (PubMed:25394321). The majority of the autoantibodies react with the two most N-terminal TSP type-1 domains (PubMed:29555830). {ECO:0000269|PubMed:25394321, ECO:0000269|PubMed:29555830}.; ","FUNCTION: Thrombospondin type-1 domain-containing protein 7A: Plays a role in actin cytoskeleton rearrangement. {ECO:0000269|PubMed:27214550}.; ",{"$nulls":4},"p.Asn1117fs","c.3349_3350insT","HIGH","1117/1657",16,{"$nulls":5},"3",null,null,"563","571","642","670",null,null,"0","0.0582",{"$nulls":5},"(THSD7A|ENSG00000005108|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","699,0","0","699","0/1","685,37","0.0512","722",null,"chr7:11424729:T:TA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0508"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TMC2","chr20:2610587","TMC2(V528I)",null,null,"transmembrane region (Helical ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs1050729550",-1,null,"FUNCTION: Probable ion channel required for the normal function of cochlear hair cells (PubMed:11850618). Component of the hair cell's mechanotransduction (MET) machinery. Involved in mechanosensitive responses of the hair cells (By similarity). {ECO:0000250|UniProtKB:E7FFT2, ECO:0000269|PubMed:11850618}.; ",{"$nulls":4},"p.Val528Ile","c.1582G>A","MODERATE","528/906",12,{"$nulls":5},"5","182","135","141","93","175","128","0","0","0","0.1406",{"$nulls":20},"2.049564","-0.09","1.465","0.999881","-0.59","0.143","0.519","0.154",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","181,0","0","181","0/1","113,20","0.1504","133",null,"chr20:2610587:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.129"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","TP53","chr17:7674220","TP53(R209Q)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In sporadic cancers; somatic mutation. TP53(R209I)), sequence variant (In sporadic cancers; somatic mutation. TP53(R209K)), sequence variant (In a sporadic cancer; somatic mutation. TP53(R209S)), sequence variant (In sporadic cancers; somatic mutation. TP53(R209T)), turn ",{"$nulls":3},255,"PASS","Missense","rs11540652",0.0002312,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg209Gln","c.626G>A","MODERATE","209/410",7,1100,{"$nulls":4},"5","712","490","541","366","623","427","0","0","0","0.1499",{"$nulls":20},"4.281887","-7.28;-7.28;.;.;.;.;.;.;.;-7.28;.;.;-7.28;-7.28;.;.;-7.28;.;.;-7.28;-7.28",".;.;.;.;.;.;.;.;.;2.935;.;2.935;2.935;2.935;.;.;2.935;.;.;.;.","0.999878;0.999994;0.999994;0.999994;0.999994;0.999994","-3.75;-3.88;.;.;.;.;.;.;.;-3.92;.;.;-3.88;-3.88;.;.;-3.92;.;.;-3.71;-3.44","1.0;.;.;.;.;.;.;.;.;1.0;.;1.0;0.994;1.0;.;.;1.0;.;.;.;1.0","0.005;0.006;.;.;.;.;.;.;.;0.006;.;.;0.006;0.006;.;.;0.006;.;.;0.008;0.007","0.946;0.933;0.935;0.934;0.931;0.898;0.935;0.935;0.929;0.921;0.928;0.933;0.932;0.932;0.94;0.885;0.921;0.928;0.914;.;.",{"$nulls":3},"ExAC_EAS_AF",0.0002312,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","688,0","0","688","0/1","397,73","0.1553","470",null,"chr17:7674220:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1557"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TP53","chr17:7674220","TP53(R209Q)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In sporadic cancers; somatic mutation. TP53(R209I)), sequence variant (In sporadic cancers; somatic mutation. TP53(R209K)), sequence variant (In a sporadic cancer; somatic mutation. TP53(R209S)), sequence variant (In sporadic cancers; somatic mutation. TP53(R209T)), turn ",{"$nulls":3},255,"PASS","Missense","rs11540652",0.0002312,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg209Gln","c.626G>A","MODERATE","209/410",7,1100,{"$nulls":4},"5","712","449","541","326","623","383","0","0","0","0.2115",{"$nulls":20},"4.281887","-7.28;-7.28;.;.;.;.;.;.;.;-7.28;.;.;-7.28;-7.28;.;.;-7.28;.;.;-7.28;-7.28",".;.;.;.;.;.;.;.;.;2.935;.;2.935;2.935;2.935;.;.;2.935;.;.;.;.","0.999878;0.999994;0.999994;0.999994;0.999994;0.999994","-3.75;-3.88;.;.;.;.;.;.;.;-3.92;.;.;-3.88;-3.88;.;.;-3.92;.;.;-3.71;-3.44","1.0;.;.;.;.;.;.;.;.;1.0;.;1.0;0.994;1.0;.;.;1.0;.;.;.;1.0","0.005;0.006;.;.;.;.;.;.;.;0.006;.;.;0.006;0.006;.;.;0.006;.;.;0.008;0.007","0.946;0.933;0.935;0.934;0.931;0.898;0.935;0.935;0.929;0.921;0.928;0.933;0.932;0.932;0.94;0.885;0.921;0.928;0.914;.;.",{"$nulls":3},"ExAC_EAS_AF",0.0002312,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","681,0","0","681","0/1","335,91","0.2136","426",null,"chr17:7674220:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2086"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","TRPM1","chr15:31029352","TRPM1(N1066fs)",null,null,"transmembrane region (Helical ), splice variant (In isoform 7. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Night blindness, congenital stationary, 1C (CSNB1C) [MIM:613216]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269|PubMed:19878917, ECO:0000269|PubMed:19896109, ECO:0000269|PubMed:19896113}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cation channel essential for the depolarizing photoresponse of retinal ON bipolar cells. It is part of the GRM6 signaling cascade. May play a role in metastasis suppression (By similarity). May act as a spontaneously active, calcium-permeable plasma membrane channel. {ECO:0000250, ECO:0000269|PubMed:11535825, ECO:0000269|PubMed:19878917, ECO:0000269|PubMed:19896109}.; ",{"$nulls":4},"p.Asn1066fs","c.3196_3199+18delAATCGTAAGTTTACATGGAATT","HIGH","1066/1642",23,{"$nulls":5},"5","572","430","433","323","532","392","0","0","0","0.0893",{"$nulls":5},"(TRPM1|ENSG00000134160|1|1.00)",{"$nulls":25},"Unknown",-1,"AR","Night blindness, congenital stationary, type 1C","Ophthalmologic",{"$nulls":3},"C2750747","0/0","668,0","0","668","0/1","430,41","0.087","471",null,"chr15:31029352:CAATTCCATGTAAACTTACGATT:C",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1084"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TTN","chr2:178554498","TTN(G29617R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Hereditary myopathy with early respiratory failure (HMERF) [MIM:603689]: Autosomal dominant, adult-onset myopathy with early respiratory muscle involvement. {ECO:0000269|PubMed:15802564}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, familial hypertrophic 9 (CMH9) [MIM:613765]: A hereditary heart disorder characterized by ventricular hypertrophy, which is usually asymmetric and often involves the interventricular septum. The symptoms include dyspnea, syncope, collapse, palpitations, and chest pain. They can be readily provoked by exercise. The disorder has inter- and intrafamilial variability ranging from benign to malignant forms with high risk of cardiac failure and sudden cardiac death. {ECO:0000269|PubMed:10462489}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cardiomyopathy, dilated 1G (CMD1G) [MIM:604145]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269|PubMed:11788824, ECO:0000269|PubMed:11846417, ECO:0000269|PubMed:16465475}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tardive tibial muscular dystrophy (TMD) [MIM:600334]: Autosomal dominant, late-onset distal myopathy. Muscle weakness and atrophy are usually confined to the anterior compartment of the lower leg, in particular the tibialis anterior muscle. Clinical symptoms usually occur at age 35-45 years or much later. {ECO:0000269|PubMed:12145747, ECO:0000269|PubMed:12891679}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-girdle muscular dystrophy 2J (LGMD2J) [MIM:608807]: An autosomal recessive degenerative myopathy characterized by progressive weakness of the pelvic and shoulder girdle muscles. Severe disability is observed within 20 years of onset. {ECO:0000269|PubMed:12145747}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Salih myopathy (SALMY) [MIM:611705]: An autosomal recessive, early-onset muscular disorder characterized by dilated cardiomyopathy, delayed motor development with generalized muscle weakness predominantly affecting proximal and distal lower limbs. Skeletal muscle biopsies show minicore-like lesions with mitochondrial depletion and sarcomere disorganization, centralized nuclei, and type 1 fiber predominance. Dystrophic changes become apparent in the second decade. Cardiac muscle biopsies show disruption of myocardial architecture, nuclear hypertrophy, and endomysial fibrosis. Sudden death may occurr due to cardiomyopathy. {ECO:0000269|PubMed:17444505}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The size and extensibility of the cross-links are the main determinants of sarcomere extensibility properties of muscle. In non-muscle cells, seems to play a role in chromosome condensation and chromosome segregation during mitosis. Might link the lamina network to chromatin or nuclear actin, or both during interphase. {ECO:0000269|PubMed:9804419}.; ",{"$nulls":4},"p.Gly29617Arg","c.88849G>C","MODERATE","29617/35991",332,{"$nulls":5},"5","599","513","454","372","518","463","0","0","0","0.067",{"$nulls":20},"3.241542","-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;.",".;.;.;3.225;.;.;3.225","1","-6.11;-6.27;.;.;-6.27;-6.27;.",".;.;.;1.0;.;.;1.0","0.003;0.002;.;.;0.002;0.002;.","0.496;0.854;0.462;0.453;0.854;0.854;0.461",{"$nulls":3},"Unknown",-1,"AD","Cardiomyopathy, familial hypertrophic 9; Cardiomyopathy, dilated, 1G","Cardiovascular; Musculoskeletal",null,"This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012].",null,"C1858763| C1837342| C0007193| C2673677| C1838244| C1861065| C1863599","0/0","572,0","0","572","0/1","460,33","0.0669","493",null,"chr2:178554498:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0806"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","TYW1","chr7:67055858","TYW1(S376A)",null,null,"splice variant (In isoform 2. )","modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N- methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ser376Ala","c.1126T>G","MODERATE","376/732",9,{"$nulls":5},"4",null,null,"233","281","317","327",null,null,"0","0.0581",{"$nulls":20},"3.502938","1.43","3.44","0.999505","-2.62","0.918",null,"0.559",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","344,0","0","344","0/1","374,23","0.0579","397",null,"chr7:67055858:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0605"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","TYW1","chr7:67055858","TYW1(S376A)",null,null,"splice variant (In isoform 2. )","modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,null,"FUNCTION: Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. Catalyzes the condensation of N- methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in wybutosine biosynthesis (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ser376Ala","c.1126T>G","MODERATE","376/732",9,{"$nulls":5},"5","361","344","233","220","319","251","0","0","0","0.1315",{"$nulls":20},"3.502938","1.43","3.44","0.999505","-2.62","0.918",null,"0.559",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","344,0","0","344","0/1","285,36","0.1121","321",null,"chr7:67055858:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1182"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","UBAP2L","chr1:154268785","UBAP2L(S1000C)",null,null,"splice variant (In isoform 2 and isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays an important role in the activity of long-term repopulating hematopoietic stem cells (LT-HSCs). {ECO:0000250|UniProtKB:Q80X50}.; ",{"$nulls":4},"p.Ser1000Cys","c.2999C>G","MODERATE","1000/1087",25,2,{"$nulls":4},"3","282","268",{"$nulls":4},"0","0",{"$nulls":22},"3.887991","1.29;.;1.29","1.1;.;1.1","0.990584","-1.93;.;-1.93","0.99;.;0.99","0.002;.;0.002","0.516;0.498;0.515",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","276,0","0","276","0/1","243,13","0.0508","256",null,"chr1:154268785:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","UBAP2L","chr1:154268785","UBAP2L(S1000C)",null,null,"splice variant (In isoform 2 and isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays an important role in the activity of long-term repopulating hematopoietic stem cells (LT-HSCs). {ECO:0000250|UniProtKB:Q80X50}.; ",{"$nulls":4},"p.Ser1000Cys","c.2999C>G","MODERATE","1000/1087",25,2,{"$nulls":4},"5","282","233","221","188","210","199","0","0","0","0.1307",{"$nulls":20},"3.887991","1.29;.;1.29","1.1;.;1.1","0.990584","-1.93;.;-1.93","0.99;.;0.99","0.002;.;0.002","0.516;0.498;0.515",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","263,0","0","263","0/1","198,26","0.1161","224",null,"chr1:154268785:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.117"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","VEGFC","chr4:176727927","VEGFC(E135*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,"DISEASE: Lymphedema, hereditary, 1D (LMPH1D) [MIM:615907]: A chronic disabling condition which results in swelling of the extremities due to altered lymphatic flow. Patients with lymphedema suffer from recurrent local infections and physical impairment. {ECO:0000269|PubMed:23410910, ECO:0000269|PubMed:24744435}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Growth factor active in angiogenesis, and endothelial cell growth, stimulating their proliferation and migration and also has effects on the permeability of blood vessels. May function in angiogenesis of the venous and lymphatic vascular systems during embryogenesis, and also in the maintenance of differentiated lymphatic endothelium in adults. Binds and activates KDR/VEGFR2 and FLT4/VEGFR3 receptors. {ECO:0000269|PubMed:20145116}.; ","level2",{"$nulls":3},"p.Glu135*","c.403G>T","HIGH","135/419",3,{"$nulls":5},"4","535","356","370","227","508","317","0","0","0","0.0726",{"$nulls":5},"(VEGFC|ENSG00000150630|1|1.00)","(VEGFC|ENSG00000150630|1|1.00)",{"$nulls":13},"7.155059",null,null,"1",{"$nulls":3},"0.972",{"$nulls":3},"Unknown",-1,"AD","Lymphedema, hereditary, ID","Dermatologic","kCANCER,kMTOR",null,null,"C4747769","0/0","511,0","0","511","0/1","318,27","0.0783","345",null,"chr4:176727927:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0749"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","VWDE","chr7:12389330","VWDE(I91N)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ile91Asn","c.272T>A","MODERATE","91/1590",3,{"$nulls":5},"5","439","482","311","325","418","455","0","0","0","0.0637",{"$nulls":20},"3.937111","-0.04","2.85","0.625834","-4.64","0.993","0.001","0.605",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","431,0","0","431","0/1","427,33","0.0717","460",null,"chr7:12389330:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0646"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","WDR11","chr10:120880861","WDR11(D567H)",null,null,"repeat (WD 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving WDR11 is found in a form of Kallmann syndrome. Translocation 46,XY,t(10;12)(q26.12;q13.11). {ECO:0000269|PubMed:20887964}.; DISEASE: Hypogonadotropic hypogonadism 14 with or without anosmia (HH14) [MIM:614858]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:20887964, ECO:0000269|PubMed:29263200}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the Hedgehog (Hh) signaling pathway, is essential for normal ciliogenesis (PubMed:29263200). Regulates the proteolytic processing of GLI3 and cooperates with the transcription factor EMX1 in the induction of downstream Hh pathway gene expression and gonadotropin-releasing hormone production (PubMed:29263200). WDR11 complex facilitates the tethering of Adaptor protein-1 complex (AP-1)-derived vesicles. WDR11 complex acts together with TBC1D23 to facilitate the golgin- mediated capture of vesicles generated using AP-1 (PubMed:29426865). {ECO:0000269|PubMed:29263200, ECO:0000269|PubMed:29426865}.; ",{"$nulls":4},"p.Asp567His","c.1699G>C","MODERATE","567/1224",13,{"$nulls":5},"5","249","1526","183","1043","213","1337","0","0","0","0.7143",{"$nulls":20},"4.2972529999999995","1.18;.","1.895;.","1","-2.68;.","0.998;.","0.007;.","0.767;.",{"$nulls":3},"Unknown",-1,"AD","Hypogonadotropic hypogonadism; Kallmann syndrome","Endocrine; Neurologic",{"$nulls":3},"C3540450| C0342384","0/0","239,0","0","239","0/1","417,1028","0.7114","1445",null,"chr10:120880861:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7114"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","WDR11","chr10:120880861","WDR11(D567H)",null,null,"repeat (WD 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving WDR11 is found in a form of Kallmann syndrome. Translocation 46,XY,t(10;12)(q26.12;q13.11). {ECO:0000269|PubMed:20887964}.; DISEASE: Hypogonadotropic hypogonadism 14 with or without anosmia (HH14) [MIM:614858]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:20887964, ECO:0000269|PubMed:29263200}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the Hedgehog (Hh) signaling pathway, is essential for normal ciliogenesis (PubMed:29263200). Regulates the proteolytic processing of GLI3 and cooperates with the transcription factor EMX1 in the induction of downstream Hh pathway gene expression and gonadotropin-releasing hormone production (PubMed:29263200). WDR11 complex facilitates the tethering of Adaptor protein-1 complex (AP-1)-derived vesicles. WDR11 complex acts together with TBC1D23 to facilitate the golgin- mediated capture of vesicles generated using AP-1 (PubMed:29426865). {ECO:0000269|PubMed:29263200, ECO:0000269|PubMed:29426865}.; ",{"$nulls":4},"p.Asp567His","c.1699G>C","MODERATE","567/1224",13,{"$nulls":5},"4","249","2186","183","1542","213","1956","0","0","0","0.6979",{"$nulls":20},"4.2972529999999995","1.18;.","1.895;.","1","-2.68;.","0.998;.","0.007;.","0.767;.",{"$nulls":3},"Unknown",-1,"AD","Hypogonadotropic hypogonadism; Kallmann syndrome","Endocrine; Neurologic",{"$nulls":3},"C3540450| C0342384","0|0","241,0","0","241","0|1","660,1452","0.6875","2112",null,"chr10:120880861:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.677"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","WDR11","chr10:120880886","WDR11(K575T)",null,null,"repeat (WD 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving WDR11 is found in a form of Kallmann syndrome. Translocation 46,XY,t(10;12)(q26.12;q13.11). {ECO:0000269|PubMed:20887964}.; DISEASE: Hypogonadotropic hypogonadism 14 with or without anosmia (HH14) [MIM:614858]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:20887964, ECO:0000269|PubMed:29263200}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the Hedgehog (Hh) signaling pathway, is essential for normal ciliogenesis (PubMed:29263200). Regulates the proteolytic processing of GLI3 and cooperates with the transcription factor EMX1 in the induction of downstream Hh pathway gene expression and gonadotropin-releasing hormone production (PubMed:29263200). WDR11 complex facilitates the tethering of Adaptor protein-1 complex (AP-1)-derived vesicles. WDR11 complex acts together with TBC1D23 to facilitate the golgin- mediated capture of vesicles generated using AP-1 (PubMed:29426865). {ECO:0000269|PubMed:29263200, ECO:0000269|PubMed:29426865}.; ",{"$nulls":4},"p.Lys575Thr","c.1724A>C","MODERATE","575/1224",13,{"$nulls":5},"5","230","1390","162","937","208","1262","0","0","0","0.7068",{"$nulls":20},"4.203182","-2.69","1.845","1","-2.95","0.999","0.005","0.824",{"$nulls":3},"Unknown",-1,"AD","Hypogonadotropic hypogonadism; Kallmann syndrome","Endocrine; Neurologic",{"$nulls":3},"C3540450| C0342384","0/0","226,0","0","226","0/1","385,952","0.712","1337",null,"chr10:120880886:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7118"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","WDR11","chr10:120880886","WDR11(K575T)",null,null,"repeat (WD 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Note=A chromosomal aberration involving WDR11 is found in a form of Kallmann syndrome. Translocation 46,XY,t(10;12)(q26.12;q13.11). {ECO:0000269|PubMed:20887964}.; DISEASE: Hypogonadotropic hypogonadism 14 with or without anosmia (HH14) [MIM:614858]: A disorder characterized by absent or incomplete sexual maturation by the age of 18 years, in conjunction with low levels of circulating gonadotropins and testosterone and no other abnormalities of the hypothalamic- pituitary axis. In some cases, it is associated with non- reproductive phenotypes, such as anosmia, cleft palate, and sensorineural hearing loss. Anosmia or hyposmia is related to the absence or hypoplasia of the olfactory bulbs and tracts. Hypogonadism is due to deficiency in gonadotropin-releasing hormone and probably results from a failure of embryonic migration of gonadotropin-releasing hormone-synthesizing neurons. In the presence of anosmia, idiopathic hypogonadotropic hypogonadism is referred to as Kallmann syndrome, whereas in the presence of a normal sense of smell, it has been termed normosmic idiopathic hypogonadotropic hypogonadism (nIHH). {ECO:0000269|PubMed:20887964, ECO:0000269|PubMed:29263200}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Involved in the Hedgehog (Hh) signaling pathway, is essential for normal ciliogenesis (PubMed:29263200). Regulates the proteolytic processing of GLI3 and cooperates with the transcription factor EMX1 in the induction of downstream Hh pathway gene expression and gonadotropin-releasing hormone production (PubMed:29263200). WDR11 complex facilitates the tethering of Adaptor protein-1 complex (AP-1)-derived vesicles. WDR11 complex acts together with TBC1D23 to facilitate the golgin- mediated capture of vesicles generated using AP-1 (PubMed:29426865). {ECO:0000269|PubMed:29263200, ECO:0000269|PubMed:29426865}.; ",{"$nulls":4},"p.Lys575Thr","c.1724A>C","MODERATE","575/1224",13,{"$nulls":5},"4","230","2005","162","1331","208","1835","0","0","0","0.685",{"$nulls":20},"4.203182","-2.69","1.845","1","-2.95","0.999","0.005","0.824",{"$nulls":3},"Unknown",-1,"AD","Hypogonadotropic hypogonadism; Kallmann syndrome","Endocrine; Neurologic",{"$nulls":3},"C3540450| C0342384","0|0","228,0","0","228","0|1","616,1341","0.6852","1957",null,"chr10:120880886:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6709"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","WDR47","chr1:109013904","WDR47(K88N)",null,null,"domain (CTLH )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys88Asn","c.264G>T","MODERATE","88/927",4,{"$nulls":5},"5","311","228","208","155","287","208","0","0","0","0.0913",{"$nulls":20},"2.713667","-0.07;-0.06;0.18;-0.1;0.18;.;.;.","2.7;2.7;.;2.7;.;.;.;.","0.999992","-2.58;-2.58;-2.35;-2.58;-2.35;-4.1;-4.1;-4.2",".;0.891;0.665;0.999;.;.;.;.","0.002;0.002;0.002;0.002;0.002;0.003;0.005;0.003","0.879;0.884;0.873;0.888;0.876;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","307,0","0","307","0/1","202,17","0.0776","219",null,"chr1:109013904:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0774"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","WDR47","chr1:109013904","WDR47(K88N)",null,null,"domain (CTLH )",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Lys88Asn","c.264G>T","MODERATE","88/927",4,{"$nulls":5},"5","311","223","208","143","287","203","0","0","0","0.1478",{"$nulls":20},"2.713667","-0.07;-0.06;0.18;-0.1;0.18;.;.;.","2.7;2.7;.;2.7;.;.;.;.","0.999992","-2.58;-2.58;-2.35;-2.58;-2.35;-4.1;-4.1;-4.2",".;0.891;0.665;0.999;.;.;.;.","0.002;0.002;0.002;0.002;0.002;0.003;0.005;0.003","0.879;0.884;0.873;0.888;0.876;.;.;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","307,0","0","307","0/1","184,33","0.1521","217",null,"chr1:109013904:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1608"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","WDR93","chr15:89743317","WDR93(E663Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu663Gln","c.1987G>C","MODERATE","663/686",17,{"$nulls":5},"5","425","289","310","207","352","235","0","0","0","0.0723",{"$nulls":20},"0.22986","1.93;1.92","0.895;.","1","-0.12","0.531","0.208;0.354","0.071;0.062",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","411,0","0","411","0/1","251,22","0.0806","273",null,"chr15:89743317:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0773"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","WEE1","chr11:9574159","WEE1(R76S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a negative regulator of entry into mitosis (G2 to M transition) by protecting the nucleus from cytoplasmically activated cyclin B1-complexed CDK1 before the onset of mitosis by mediating phosphorylation of CDK1 on 'Tyr-15'. Specifically phosphorylates and inactivates cyclin B1-complexed CDK1 reaching a maximum during G2 phase and a minimum as cells enter M phase. Phosphorylation of cyclin B1-CDK1 occurs exclusively on 'Tyr-15' and phosphorylation of monomeric CDK1 does not occur. Its activity increases during S and G2 phases and decreases at M phase when it is hyperphosphorylated. A correlated decrease in protein level occurs at M/G1 phase, probably due to its degradation.; ","level2",{"$nulls":3},"p.Arg76Ser","c.226C>A","MODERATE","76/646",1,{"$nulls":5},"3",null,null,"63","48",{"$nulls":26},"2.020116","0.65",null,"0.777278","-0.33","0.218","0.129","0.152",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE",{"$nulls":3},"0/0","84,0","0","84","0/1","51,3","0.0556","54",null,"chr11:9574159:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0625"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","WEE1","chr11:9574159","WEE1(R76S)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Acts as a negative regulator of entry into mitosis (G2 to M transition) by protecting the nucleus from cytoplasmically activated cyclin B1-complexed CDK1 before the onset of mitosis by mediating phosphorylation of CDK1 on 'Tyr-15'. Specifically phosphorylates and inactivates cyclin B1-complexed CDK1 reaching a maximum during G2 phase and a minimum as cells enter M phase. Phosphorylation of cyclin B1-CDK1 occurs exclusively on 'Tyr-15' and phosphorylation of monomeric CDK1 does not occur. Its activity increases during S and G2 phases and decreases at M phase when it is hyperphosphorylated. A correlated decrease in protein level occurs at M/G1 phase, probably due to its degradation.; ","level2",{"$nulls":3},"p.Arg76Ser","c.226C>A","MODERATE","76/646",1,{"$nulls":5},"5","85","51","63","43","66","36","0","0","0","0.1667",{"$nulls":20},"2.020116","0.65",null,"0.777278","-0.33","0.218","0.129","0.152",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCELL_CYCLE",{"$nulls":3},"0/0","84,0","0","84","0/1","40,9","0.1837","49",null,"chr11:9574159:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.186"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","XDH","chr2:31403104","XDH(G47fs)",null,null,"domain (2Fe-2S ferredoxin-type ), strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Xanthinuria 1 (XAN1) [MIM:278300]: A disorder characterized by excretion of very large amounts of xanthine in the urine and a tendency to form xanthine stones. Uric acid is strikingly diminished in serum and urine. XAN1 is due to isolated xanthine dehydrogenase deficiency. Patients can metabolize allopurinol. {ECO:0000269|PubMed:10844591, ECO:0000269|PubMed:11379872, ECO:0000269|PubMed:14551354, ECO:0000269|PubMed:9153281}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro). {ECO:0000269|PubMed:17301077}.; ",{"$nulls":4},"p.Gly47fs","c.140delG","HIGH","47/1333",3,{"$nulls":5},"4",null,null,"429","418","534","534",null,null,"0","0.0581",{"$nulls":31},"Unknown",-1,"AR","Xanthinuria, type I","Biochemical; Musculoskeletal; Renal",{"$nulls":3},"C0268118","0/0","554,0","0","554","0/1","533,31","0.055","564",null,"chr2:31403104:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.055"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","XDH","chr2:31403104","XDH(G47fs)",null,null,"domain (2Fe-2S ferredoxin-type ), strand ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Xanthinuria 1 (XAN1) [MIM:278300]: A disorder characterized by excretion of very large amounts of xanthine in the urine and a tendency to form xanthine stones. Uric acid is strikingly diminished in serum and urine. XAN1 is due to isolated xanthine dehydrogenase deficiency. Patients can metabolize allopurinol. {ECO:0000269|PubMed:10844591, ECO:0000269|PubMed:11379872, ECO:0000269|PubMed:14551354, ECO:0000269|PubMed:9153281}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro). {ECO:0000269|PubMed:17301077}.; ",{"$nulls":4},"p.Gly47fs","c.140delG","HIGH","47/1333",3,{"$nulls":5},"3",null,null,"429","322",{"$nulls":37},"Unknown",-1,"AR","Xanthinuria, type I","Biochemical; Musculoskeletal; Renal",{"$nulls":3},"C0268118","0/0","554,0","0","554","0/1","393,27","0.0643","420",null,"chr2:31403104:GC:G",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0559"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","XPR1","chr1:180811461","XPR1(V246L)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense","rs375661577",0.000152,"DISEASE: Basal ganglia calcification, idiopathic, 6 (IBGC6) [MIM:616413]: A form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. {ECO:0000269|PubMed:25938945}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in phosphate homeostasis. Mediates phosphate export from the cell (PubMed:23791524, PubMed:25938945). Binds inositol hexakisphosphate (Ins6P) and similar inositol polyphosphates, such as 5-diphospho-inositol pentakisphosphate (5- InsP7); these are important intracellular signaling molecules (PubMed:27080106). {ECO:0000250|UniProtKB:Q9Z0U0, ECO:0000269|PubMed:23791524, ECO:0000269|PubMed:25938945, ECO:0000269|PubMed:27080106}.; ",{"$nulls":4},"p.Val246Leu","c.736G>T","MODERATE","246/696",7,1,{"$nulls":4},"5","548","487","363","328","505","451","0","0","0","0.1641",{"$nulls":20},"3.106138","0.85;.","2.635","0.999985;0.999995","-2.19;-2.12","0.826;0.936","0.024;0.008","0.414;0.42",{"$nulls":3},"ExAC_FIN_AF",0.000152,{"$nulls":6},"C4225335","0/0","529,0","0","529","0/1","387,81","0.1731","468",null,"chr1:180811461:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1646"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","XPR1","chr1:180811461","XPR1(V246L)",null,null,"transmembrane region (Helical )",{"$nulls":3},255,"PASS","Missense","rs375661577",0.000152,"DISEASE: Basal ganglia calcification, idiopathic, 6 (IBGC6) [MIM:616413]: A form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. {ECO:0000269|PubMed:25938945}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in phosphate homeostasis. Mediates phosphate export from the cell (PubMed:23791524, PubMed:25938945). Binds inositol hexakisphosphate (Ins6P) and similar inositol polyphosphates, such as 5-diphospho-inositol pentakisphosphate (5- InsP7); these are important intracellular signaling molecules (PubMed:27080106). {ECO:0000250|UniProtKB:Q9Z0U0, ECO:0000269|PubMed:23791524, ECO:0000269|PubMed:25938945, ECO:0000269|PubMed:27080106}.; ",{"$nulls":4},"p.Val246Leu","c.736G>T","MODERATE","246/696",7,1,{"$nulls":4},"5","548","465","363","304","505","421","0","0","0","0.247",{"$nulls":20},"3.106138","0.85;.","2.635","0.999985;0.999995","-2.19;-2.12","0.826;0.936","0.024;0.008","0.414;0.42",{"$nulls":3},"ExAC_FIN_AF",0.000152,{"$nulls":6},"C4225335","0/0","533,0","0","533","0/1","340,107","0.2394","447",null,"chr1:180811461:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.25"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","YTHDC2","chr5:113564033","YTHDC2(P873T)",{"$nulls":6},255,"PASS","Missense","rs193921121",-1,null,"FUNCTION: 3'-5' RNA helicase that plays a key role in the male and female germline by promoting transition from mitotic to meiotic divisions in stem cells (PubMed:26318451, PubMed:29033321). Specifically recognizes and binds N6-methyladenosine (m6A)- containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs that plays a role in the efficiency of RNA processing and stability (PubMed:26318451, PubMed:29033321). Essential for ensuring a successful progression of the meiotic program in the germline by regulating the level of m6A-containing RNAs (By similarity). Acts by binding and promoting degradation of m6A-containing mRNAs: the 3'-5' RNA helicase activity is required for this process and RNA degradation may be mediated by XRN1 exoribonuclease (PubMed:29033321). Required for both spermatogenesis and oogenesis (By similarity). {ECO:0000250|UniProtKB:B2RR83, ECO:0000269|PubMed:26318451, ECO:0000269|PubMed:29033321}.; ",{"$nulls":4},"p.Pro873Thr","c.2617C>A","MODERATE","873/1430",20,1,{"$nulls":4},"4","1064","912","732","624","945","800","0","0","0","0.075",{"$nulls":20},"3.6954789999999997","0.91","2.79","1","-6.68","0.989","0.063","0.885",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1015,0","0","1015","0/1","800,65","0.0751","865",null,"chr5:113564033:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0705"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","YTHDC2","chr5:113564033","YTHDC2(P873T)",{"$nulls":6},255,"PASS","Missense","rs193921121",-1,null,"FUNCTION: 3'-5' RNA helicase that plays a key role in the male and female germline by promoting transition from mitotic to meiotic divisions in stem cells (PubMed:26318451, PubMed:29033321). Specifically recognizes and binds N6-methyladenosine (m6A)- containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs that plays a role in the efficiency of RNA processing and stability (PubMed:26318451, PubMed:29033321). Essential for ensuring a successful progression of the meiotic program in the germline by regulating the level of m6A-containing RNAs (By similarity). Acts by binding and promoting degradation of m6A-containing mRNAs: the 3'-5' RNA helicase activity is required for this process and RNA degradation may be mediated by XRN1 exoribonuclease (PubMed:29033321). Required for both spermatogenesis and oogenesis (By similarity). {ECO:0000250|UniProtKB:B2RR83, ECO:0000269|PubMed:26318451, ECO:0000269|PubMed:29033321}.; ",{"$nulls":4},"p.Pro873Thr","c.2617C>A","MODERATE","873/1430",20,1,{"$nulls":4},"4","1064","773","732","522","946","680","0","0","0","0.0765",{"$nulls":20},"3.6954789999999997","0.91","2.79","1","-6.68","0.989","0.063","0.885",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","1015,0","0","1015","0/1","669,52","0.0721","721",null,"chr5:113564033:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0709"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ZNF208","chr19:21971673","ZNF208(A1093_K1120del)",null,null,"zinc finger region (C2H2-type 33 )","zinc-finger-region:C2H2-type_34","LOW",null,255,"PASS","Inframe Indel",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ala1093_Lys1120del","c.3277_3360delGCTTTCAACTGGTCCTCAAACCTTATGGAACATAAGAGAATTCATACTGGAGAGAAACCCTACAAATGTGAAGAATGTGGCAAA","MODERATE","1093/1280",4,{"$nulls":20},"21971757",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr19:21971673:TTTTGCCACATTCTTCACATTTGTAGGGTTTCTCTCCAGTATGAATTCTCTTATGTTCCATAAGGTTTGAGGACCAGTTGAAAGC:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ZNF528","chr19:52406599","ZNF528(A76E)",null,null,"domain (KRAB ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Ala76Glu","c.227C>A","MODERATE","76/628",6,{"$nulls":5},"4","284","281","179","180","257","258","0.0035","0.0035","0","0.062",{"$nulls":20},"-0.494261","5.56;5.64;3.53;5.72;5.69",".;.;0.415;.;.","1","-3.62;-3.77;-0.85;.;.",".;.;0.728;.;.","0.008;0.009;0.793;.;.","0.121;.;0.153;0.118;0.106",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","275,0","0","275","0/1","248,20","0.0746","268",null,"chr19:52406599:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","LOWQC","tumor","significant","0.0667"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ZNF598","chr16:2000102","ZNF598(E428*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase that plays a key role in the ribosome quality control (RQC), a pathway that takes place when a ribosome has stalled during translation (PubMed:28065601, PubMed:28132843). Required for ribosomes to terminally stall during translation of poly(A) sequences by mediating monoubiquitination of 40S ribosomal protein RPS10/eS10, RPS20/uS10 and RPS3/uS3 (PubMed:28065601, PubMed:28132843). Stalling precludes synthesis of a long poly-lysine tail and initiates the RQC pathway to degrade the potentially detrimental aberrant nascent polypeptide (PubMed:28065601, PubMed:28132843). Also acts as a component of the 4EHP-GYF2 complex, a multiprotein complex that acts as a repressor of translation initiation (PubMed:22751931). {ECO:0000269|PubMed:22751931, ECO:0000269|PubMed:28065601, ECO:0000269|PubMed:28132843}.; ",{"$nulls":4},"p.Glu428*","c.1282G>T","HIGH","428/849",9,{"$nulls":5},"5","262","233","206","175","233","199","0","0","0","0.0854",{"$nulls":5},"(ZNF598|ENSG00000167962|1|1.00)","(ZNF598|ENSG00000167962|1|1.00)",{"$nulls":13},"8.502056",null,null,"1",{"$nulls":3},"0.137",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","252,0","0","252","0/1","201,22","0.0987","223",null,"chr16:2000102:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1029"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ZNF598","chr16:2000102","ZNF598(E428*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase that plays a key role in the ribosome quality control (RQC), a pathway that takes place when a ribosome has stalled during translation (PubMed:28065601, PubMed:28132843). Required for ribosomes to terminally stall during translation of poly(A) sequences by mediating monoubiquitination of 40S ribosomal protein RPS10/eS10, RPS20/uS10 and RPS3/uS3 (PubMed:28065601, PubMed:28132843). Stalling precludes synthesis of a long poly-lysine tail and initiates the RQC pathway to degrade the potentially detrimental aberrant nascent polypeptide (PubMed:28065601, PubMed:28132843). Also acts as a component of the 4EHP-GYF2 complex, a multiprotein complex that acts as a repressor of translation initiation (PubMed:22751931). {ECO:0000269|PubMed:22751931, ECO:0000269|PubMed:28065601, ECO:0000269|PubMed:28132843}.; ",{"$nulls":4},"p.Glu428*","c.1282G>T","HIGH","428/849",9,{"$nulls":5},"5","262","185","206","139","233","156","0","0","0","0.141",{"$nulls":5},"(ZNF598|ENSG00000167962|1|1.00)","(ZNF598|ENSG00000167962|1|1.00)",{"$nulls":13},"8.502056",null,null,"1",{"$nulls":3},"0.137",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","251,0","0","251","0/1","152,30","0.1648","182",null,"chr16:2000102:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1727"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ZNF791","chr19:12628096","ZNF791(E189D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu189Asp","c.567A>T","MODERATE","189/576",4,{"$nulls":5},"5","411","410","305","290","268","251","0","0","0","0.0837",{"$nulls":20},"1.205927","1.97","1.76;.","0.999694;0.999978;0.999959;0.999932","-2.69;.","0.772;.","0.106;.","0.05;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","398,0","0","398","0/1","375,28","0.0695","403",null,"chr19:12628096:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0828"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ZNF791","chr19:12628096","ZNF791(E189D)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Glu189Asp","c.567A>T","MODERATE","189/576",4,{"$nulls":5},"5","411","352","305","247","267","230","0","0","0","0.0696",{"$nulls":20},"1.205927","1.97","1.76;.","0.999694;0.999978;0.999959;0.999932","-2.69;.","0.772;.","0.106;.","0.05;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","394,0","0","394","0/1","315,27","0.0789","342",null,"chr19:12628096:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0729"]
["11JZ","T10","JLPIKTOR_JLPIKTOR_17113011JZ","ZSWIM4","chr19:13799897","ZSWIM4(A111S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala111Ser","c.331G>T","MODERATE","111/989",2,{"$nulls":5},"4","420","375","303","265",null,null,"0","0",{"$nulls":22},"1.7780740000000002","0.86","1.8","0.859059","-0.83","0.397","0.34","0.176",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","412,0","0","412","0/1","342,27","0.0732","369",null,"chr19:13799897:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T10_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0679"]
["11JZ","T9_","JLPIKTOR_JLPIKTOR_17113011JZ","ZSWIM4","chr19:13799897","ZSWIM4(A111S)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ala111Ser","c.331G>T","MODERATE","111/989",2,{"$nulls":5},"4","420","306","303","218",null,null,"0","0",{"$nulls":22},"1.7780740000000002","0.86","1.8","0.859059","-0.83","0.397","0.34","0.176",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","411,0","0","411","0/1","271,26","0.0875","297",null,"chr19:13799897:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113011JZ","somatic","somatic","JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113011JZ/somatic/JLPIKTOR_17113011JZ_1_PB_WBC_C7_A3S7X-JLPIKTOR_17113011JZ_1_BE_Whole_T9_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.078"]

{"sheet":"12GW","index":9,"n_rows":204,"n_cols":107,"rows_kept":204}
["Patient","Pre/Post ID","ProjectRun","Gene (HGNC)","chr:pos","effect","SV Pair Coordinates","LOG2FC (CNA)","Codon Info Uniprot","Uniprot Codon Features","NextProt Feature Strength","NextProt Feature","Quality","insert filter","aberration name","dbSNP Identifier (142)","Maximum Population Allele Freq","Disease Description","Functional Description","Panel or List Membership","Drug Rule","Drug Rule Evidence","Drug Rule Indication","HGVS","HGVS (cDNA)","Functional Impact","Distance","Exon Number","COSMIC Count","GBM_TCGA","BRCA_TCGA","LUAD_TCGA","SKCM_TCGA","MergedVCF Caller Count","STRELKA DP1","STRELKA DP2","VARDICT_S1_DP","VARDICT_S2_DP","LANCET_S1_DP","LANCET_S2_DP","STRELKA2_S1_AR","STRELKA2_S2_AR","LANCET_S1_AR","LANCET_S2_AR","ARDIFF","TumorAlleleRatio","NormalAlleleRatio","SvType","END","LOF Transcript Info","NMD Transcript Info","FUSED_GENE","FPKM1","FPKM2","QVALUE","PVALUE","BPGENE1","BPGENE2","cnvLength","LOG2FC in cnv file","LOG2FC in cuffdiff file","PVALUE in cuffdiff file","LOG2FC in deseq file","PVALUE in deseq file","CADD Score","FATHMM Score","Mutation Assessor Score","MutationTaster Score","PROVEAN Score","Polyphen2_HDIV Score","Sift Score","VEST4 Score","Clinvar Significance","Clinvar Review Status","Clinvar Disease Known Variant","Max PopFreq Database Hit","Max Pop Freq","CGD Inheritance","CGD Condition","CGD Manifestation","Level2 Hit","Refseq description","Pobability Haploinsufficiency","Clinvar info on gene","JLPIKTOR_17113001TL_1_PB_WBC_C7Genotype","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Depth","JLPIKTOR_17113001TL_1_PB_WBC_C7Allele Ratio","JLPIKTOR_17113001TL_1_PB_WBC_C7 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Genotype","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 Allele Ratio","JLPIKTOR_17113001TL_1_BE_Whole_T10 Depth","JLPIKTOR_17113001TL_1_BE_Whole_T10 CGA SOM Score","biomarker","biomarkerCount","dbFreq","Variant Type","studyPatient","sample","tissue","filename","filepath","filetype","old aberration filter","assay","Impact","vardict Allele Frequency"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ABCB1","chr7:87549910","ABCB1(E499Q)",null,null,"topological domain (Cytoplasmic ), domain (ABC transporter 1 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Inflammatory bowel disease 13 (IBD13) [MIM:612244]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells.; ","tcga-gbm",{"$nulls":3},"p.Glu499Gln","c.1495G>C","MODERATE","499/1280",14,{"$nulls":5},"4","572","515","428","394","491","430","0","0","0","0.3093",{"$nulls":20},"3.830363",".;-1.96;-1.96","0.955;0.955;.","1",".;-2.66;-2.58","1.0;1.0;.",".;0.022;0.01","0.361;0.511;0.356",{"$nulls":3},"Unknown",-1,"AD","Colchicine metabolism, association with","General",{"$nulls":3},"C2677101| C1861502","0/0","537,0","0","537","0/1","352,157","0.3084","509",null,"chr7:87549910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3122"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ABCB1","chr7:87549910","ABCB1(E499Q)",null,null,"topological domain (Cytoplasmic ), domain (ABC transporter 1 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Inflammatory bowel disease 13 (IBD13) [MIM:612244]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug-resistant cells.; ","tcga-gbm",{"$nulls":3},"p.Glu499Gln","c.1495G>C","MODERATE","499/1280",14,{"$nulls":5},"4","572","578","428","442","487","500","0","0","0","0.384",{"$nulls":20},"3.830363",".;-1.96;-1.96","0.955;0.955;.","1",".;-2.66;-2.58","1.0;1.0;.",".;0.022;0.01","0.361;0.511;0.356",{"$nulls":3},"Unknown",-1,"AD","Colchicine metabolism, association with","General",{"$nulls":3},"C2677101| C1861502","0/0","538,0","0","538","0/1","343,204","0.3729","547",null,"chr7:87549910:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3756"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ABCF1","chr6:30583879","ABCF1(L364R)",null,null,"domain (ABC transporter 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform 2 is required for efficient Cap- and IRES- mediated mRNA translation initiation. Isoform 2 is not involved in the ribosome biogenesis. {ECO:0000269|PubMed:19570978}.; ",{"$nulls":4},"p.Leu364Arg","c.1091T>G","MODERATE","364/845",12,{"$nulls":5},"5","122","108","94","70","114","97","0","0","0","0.6186",{"$nulls":20},"4.360209","-2.74;-2.94","1.9;.","1","-3.9;-3.77","1.0;.","0.025;0.038","0.952;0.767",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","120,0","0","120","0/1","41,65","0.6132","106",null,"chr6:30583879:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6429"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ABCF1","chr6:30583879","ABCF1(L364R)",null,null,"domain (ABC transporter 1 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Isoform 2 is required for efficient Cap- and IRES- mediated mRNA translation initiation. Isoform 2 is not involved in the ribosome biogenesis. {ECO:0000269|PubMed:19570978}.; ",{"$nulls":4},"p.Leu364Arg","c.1091T>G","MODERATE","364/845",12,{"$nulls":5},"5","122","103","94","66","114","93","0","0","0","0.5914",{"$nulls":20},"4.360209","-2.74;-2.94","1.9;.","1","-3.9;-3.77","1.0;.","0.025;0.038","0.952;0.767",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","119,0","0","119","0/1","45,57","0.5588","102",null,"chr6:30583879:T:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5303"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ABHD8","chr19:17301180","ABHD8(G146E)",{"$nulls":6},255,"PASS","Missense","rs1369864977",-1,{"$nulls":6},"p.Gly146Glu","c.437G>A","MODERATE","146/439",2,{"$nulls":5},"5","490","554","358","400","413","452","0","0","0","0.2854",{"$nulls":20},"1.045005","1.55;.","1.5;.","0.99789","0.36;.","0.063;.","0.772;.","0.316;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","479,0","0","479","0/1","380,155","0.2897","535",null,"chr19:17301180:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2925"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ABHD8","chr19:17301180","ABHD8(G146E)",{"$nulls":6},255,"PASS","Missense","rs1369864977",-1,{"$nulls":6},"p.Gly146Glu","c.437G>A","MODERATE","146/439",2,{"$nulls":5},"5","490","505","358","374","415","409","0","0","0","0.3178",{"$nulls":20},"1.045005","1.55;.","1.5;.","0.99789","0.36;.","0.063;.","0.772;.","0.316;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","479,0","0","479","0/1","329,160","0.3272","489",null,"chr19:17301180:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3182"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ADAMTS4","chr1:161191151","ADAMTS4(A834V)",null,null,"region of interest (Spacer ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs114600134",0.000992063492063492,null,"FUNCTION: Cleaves aggrecan, a cartilage proteoglycan, and may be involved in its turnover. May play an important role in the destruction of aggrecan in arthritic diseases. Could also be a critical factor in the exacerbation of neurodegeneration in Alzheimer disease. Cleaves aggrecan at the '392-Glu-|-Ala-393' site.; ",{"$nulls":4},"p.Ala834Val","c.2501C>T","MODERATE","834/837",9,2,{"$nulls":4},"5","681","921","482","670","588","790","0.0015","0.0015","0","0.0861",{"$nulls":20},"0.99508","0.08",null,"0.997194","0.94",null,"0.281","0.059",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":7},"0/0","664,1","0.0015","665","0/1","790,75","0.0867","865",null,"chr1:161191151:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0836"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","AMOTL1","chr11:94800183","AMOTL1(L332fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Inhibits the Wnt/beta-catenin signaling pathway, probably by recruiting CTNNB1 to recycling endosomes and hence preventing its translocation to the nucleus. {ECO:0000269|PubMed:22362771}.; ",{"$nulls":4},"p.Leu332fs","c.994delC","HIGH","332/956",3,{"$nulls":5},"3","439","1177","316","847",null,null,"0","0",{"$nulls":7},"(AMOTL1|ENSG00000166025|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a peripheral membrane protein that is a component of tight junctions or TJs. TJs form an apical junctional structure and act to control paracellular permeability and maintain cell polarity. This protein is related to angiomotin, an angiostatin binding protein that regulates endothelial cell migration and capillary formation. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","412,1","0.0024","413","0/1","938,152","0.1394","1090",null,"chr11:94800183:AC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1251"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","AMOTL1","chr11:94800183","AMOTL1(L332fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Inhibits the Wnt/beta-catenin signaling pathway, probably by recruiting CTNNB1 to recycling endosomes and hence preventing its translocation to the nucleus. {ECO:0000269|PubMed:22362771}.; ",{"$nulls":4},"p.Leu332fs","c.994delC","HIGH","332/956",3,{"$nulls":5},"4","439","1023","316","733",null,null,"0","0",{"$nulls":7},"(AMOTL1|ENSG00000166025|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":4},"The protein encoded by this gene is a peripheral membrane protein that is a component of tight junctions or TJs. TJs form an apical junctional structure and act to control paracellular permeability and maintain cell polarity. This protein is related to angiomotin, an angiostatin binding protein that regulates endothelial cell migration and capillary formation. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","412,1","0.0024","413","0/1","823,119","0.1263","942",null,"chr11:94800183:AC:A",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1132"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ANKRD53","chr2:70984992","ANKRD53(D429H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for normal progression through mitosis. Involved in chromosome alignment and cytokinesis via regulation of microtubules polymerization. {ECO:0000269|PubMed:26820536}.; ",{"$nulls":4},"p.Asp429His","c.1285G>C","MODERATE","429/530",6,{"$nulls":5},"5","600","524","474","417","514","441","0","0","0","0.3651",{"$nulls":20},"2.01078","-0.36;-0.47",".;1.845","1","-2.47;-2.58",".;0.997","0.006;0.005","0.343;0.211",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","593,0","0","593","0/1","326,192","0.3707","518",null,"chr2:70984992:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3717"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ANKRD53","chr2:70984992","ANKRD53(D429H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for normal progression through mitosis. Involved in chromosome alignment and cytokinesis via regulation of microtubules polymerization. {ECO:0000269|PubMed:26820536}.; ",{"$nulls":4},"p.Asp429His","c.1285G>C","MODERATE","429/530",6,{"$nulls":5},"5","600","689","474","535","516","575","0","0","0","0.327",{"$nulls":20},"2.01078","-0.36;-0.47",".;1.845","1","-2.47;-2.58",".;0.997","0.006;0.005","0.343;0.211",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","590,0","0","590","0/1","461,226","0.329","687",null,"chr2:70984992:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.329"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ANO5","chr11:22257708","ANO5(T454M)",null,null,"topological domain (Cytoplasmic ), sequence variant (In LGMDR12. ), sequence variant (In LGMDR12. )",{"$nulls":3},255,"PASS","Missense","rs148698633",1.745E-3,"DISEASE: Limb-girdle muscular dystrophy 2L (LGMD2L) [MIM:611307]: An autosomal recessive degenerative myopathy characterized by proximal weakness, weakness of the hip and shoulder girdles and prominent asymmetrical quadriceps femoris and biceps brachii atrophy. {ECO:0000269|PubMed:20096397, ECO:0000269|PubMed:22499103, ECO:0000269|PubMed:25864073, ECO:0000269|PubMed:25891276}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Miyoshi muscular dystrophy 3 (MMD3) [MIM:613319]: A late- onset muscular dystrophy characterized by distal muscle weakness of the lower limbs, calf muscle discomfort and weakness, quadriceps atrophy. Muscle weakness and atrophy may be asymmetric. {ECO:0000269|PubMed:20096397, ECO:0000269|PubMed:22499103}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Does not exhibit calcium-activated chloride channel (CaCC) activity. {ECO:0000269|PubMed:20056604, ECO:0000269|PubMed:23047743}.; ",{"$nulls":4},"p.Thr454Met","c.1361C>T","MODERATE","454/913",14,3,{"$nulls":4},"4","603","591","404","383","541","528","0","0","0","0.0663",{"$nulls":20},"0.711989","-0.08","1.61","1","-1.15","0.023","0.021","0.224",{"$nulls":3},"ExAC_EAS_AF",1.745E-3,"AR","Gnathodiaphyseal dysplasia","Allergy/Immunology/Infectious; Musculoskeletal",null,"This gene encodes a member of the anoctamin family of transmembrane proteins. The encoded protein is likely a calcium activated chloride channel. Mutations in this gene have been associated with gnathodiaphyseal dysplasia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009].",null,"C1969785| C2750076| C1833736","0/0","560,0","0","560","0/1","513,38","0.069","551",null,"chr11:22257708:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0627"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ARAF","chrX:47563260","ARAF(S44C)",null,null,"domain (RBD ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade. {ECO:0000269|PubMed:22609986}.; ","gedi|foundationOne|level2","[ \"Sorafenib\" , \"Trametinib\"]","[ \"Sorafenib\" , \"Trametinib\"]","[ \"Sorafenib\" , \"Trametinib\"]","p.Ser44Cys","c.131C>G","MODERATE","44/609",3,{"$nulls":5},"4","607","531","449","366","515","446","0","0","0","0.3722",{"$nulls":20},"2.848611","-3.41;-0.91;-3.41",".;0.535;0.535","0.998419","-0.61;0.2;-0.61",".;0.049;.","0.379;0.453;0.435","0.17;0.169;0.318",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kERBB",{"$nulls":3},"0/0","599,0","0","599","0/1","324,186","0.3647","510",null,"chrX:47563260:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3579"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ARAF","chrX:47563260","ARAF(S44C)",null,null,"domain (RBD ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May also regulate the TOR signaling cascade. {ECO:0000269|PubMed:22609986}.; ","gedi|foundationOne|level2","[ \"Sorafenib\" , \"Trametinib\"]","[ \"Sorafenib\" , \"Trametinib\"]","[ \"Sorafenib\" , \"Trametinib\"]","p.Ser44Cys","c.131C>G","MODERATE","44/609",3,{"$nulls":5},"4","607","668","449","476","516","556","0","0","0","0.3165",{"$nulls":20},"2.848611","-3.41;-0.91;-3.41",".;0.535;0.535","0.998419","-0.61;0.2;-0.61",".;0.049;.","0.379;0.453;0.435","0.17;0.169;0.318",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kCANCER,kERBB",{"$nulls":3},"0/0","596,0","0","596","0/1","437,195","0.3085","632",null,"chrX:47563260:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3046"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ARL8A","chr1:202144537","ARL8A(F12L)",null,null,"intramembrane region (Note=Mediates targeting to membranes ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in lysosomes motility. Alternatively, may play a role in chromosome segregation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Phe12Leu","c.36C>G","MODERATE","12/186",1,{"$nulls":5},"5","529","375","339","248","458","313","0","0","0","0.3482",{"$nulls":20},"2.130766","0.3;.","-0.465;.","1","0.36;.","0.0;.","1.0;.","0.343;0.32",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","512,0","0","512","0/1","232,132","0.3626","364",null,"chr1:202144537:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3589"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ARL8A","chr1:202144537","ARL8A(F12L)",null,null,"intramembrane region (Note=Mediates targeting to membranes ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in lysosomes motility. Alternatively, may play a role in chromosome segregation (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Phe12Leu","c.36C>G","MODERATE","12/186",1,{"$nulls":5},"5","529","557","339","373","459","442","0","0","0","0.509",{"$nulls":20},"2.130766","0.3;.","-0.465;.","1","0.36;.","0.0;.","1.0;.","0.343;0.32",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","512,0","0","512","0/1","266,280","0.5128","546",null,"chr1:202144537:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.496"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ASCC2","chr22:29804643","ASCC2(E450K)",{"$nulls":6},255,"PASS","Missense","rs1266995022",-1,null,"FUNCTION: Plays a role in DNA damage repair as component of the ASCC complex. Recruits ASCC3 and ALKBH3 to sites of DNA damage by binding to polyubiquitinated proteins that have 'Lys-63'-linked polyubiquitin chains (PubMed:29144457). Part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation (PubMed:12077347). {ECO:0000269|PubMed:12077347, ECO:0000269|PubMed:29144457}.; ",{"$nulls":4},"p.Glu450Lys","c.1348G>A","MODERATE","450/757",13,{"$nulls":5},"4","402","392","352","343","272","294","0","0","0","0.4252",{"$nulls":20},"1.935969","3.06;3.05;3.06","1.845;.;1.845","0.999845","-0.98","0.021;.;0.021","0.328;0.247;0.328","0.297;0.349;0.297",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","393,0","0","393","0/1","241,143","0.3724","384",null,"chr22:29804643:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3644"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ASCC2","chr22:29804643","ASCC2(E450K)",{"$nulls":6},255,"PASS","Missense","rs1266995022",-1,null,"FUNCTION: Plays a role in DNA damage repair as component of the ASCC complex. Recruits ASCC3 and ALKBH3 to sites of DNA damage by binding to polyubiquitinated proteins that have 'Lys-63'-linked polyubiquitin chains (PubMed:29144457). Part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation (PubMed:12077347). {ECO:0000269|PubMed:12077347, ECO:0000269|PubMed:29144457}.; ",{"$nulls":4},"p.Glu450Lys","c.1348G>A","MODERATE","450/757",13,{"$nulls":5},"4","402","464","352","398","271","342","0","0","0","0.4006",{"$nulls":20},"1.935969","3.06;3.05;3.06","1.845;.;1.845","0.999845","-0.98","0.021;.;0.021","0.328;0.247;0.328","0.297;0.349;0.297",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","395,0","0","395","0/1","313,141","0.3106","454",null,"chr22:29804643:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3065"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","B2M","chr15:44715583","B2M(F76L)",null,null,"domain (Ig-like C1-type ), disulfide bond , strand ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Immunodeficiency 43 (IMD43) [MIM:241600]: A disorder characterized by marked reduction in serum concentrations of immunoglobulins and albumin, and hypoproteinemia due to hypercatabolism. Patients may suffer from recurrent respiratory tract infections and severe skin disease. {ECO:0000269|PubMed:16549777}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Amyloidosis 8 (AMYL8) [MIM:105200]: A form of hereditary generalized amyloidosis. Clinical features include extensive visceral amyloid deposits, renal amyloidosis resulting in nephrotic syndrome, arterial hypertension, hepatosplenomegaly, cholestasis, petechial skin rash. There is no involvement of the nervous system. {ECO:0000269|PubMed:22693999}. Note=The disease is caused by mutations affecting the gene represented in this entry. Apart from the presence of causative mutations, beta-2- microglobulin may adopt the fibrillar configuration of amyloid when its serum levels are persistently high. High beta(2)- microglobulin serum levels result in amyloidosis in patients on long-term hemodialysis (PubMed:7918443). In contrast to patients with dialysis-related amyloidosis, patients with hereditary amyloidosis have normal circulating concentrations of beta2- microglobulin (PubMed:22693999). {ECO:0000269|PubMed:22693999, ECO:0000269|PubMed:7918443}.; ","FUNCTION: Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system. Exogenously applied M.tuberculosis EsxA or EsxA-EsxB (or EsxA expressed in host) binds B2M and decreases its export to the cell surface (total protein levels do not change), probably leading to defects in class I antigen presentation (PubMed:25356553). {ECO:0000269|PubMed:25356553}.; ","gedi",{"$nulls":3},"p.Phe76Leu","c.228C>G","MODERATE","76/119",2,{"$nulls":5},"5","607","309","445","226","525","264","0","0","0","0.5644",{"$nulls":20},"3.923406",".;3.12;3.12;.",".;2.995;2.995;2.995","0.99992",".;-5.81;-5.81;.",".;1.0;1.0;1.0",".;0.0;0.0;.","0.754;0.732;0.732;.",{"$nulls":3},"Unknown",-1,"AR","Hypoproteinemia, hypercatabolic ","Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Neurologic; Renal",{"$nulls":3},"C0268389| C1855796","0/0","592,0","0","592","0/1","127,168","0.5695","295",null,"chr15:44715583:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5929"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","BCAP29","chr7:107618411","BCAP29(V285L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in anterograde transport of membrane proteins from the endoplasmic reticulum to the Golgi. May be involved in CASP8-mediated apoptosis (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Val285Leu","c.853G>C","MODERATE","285/348",8,{"$nulls":5},"5","234","206","177","155","182","153","0","0","0","0.2288",{"$nulls":20},"0.602944",null,null,"1;1;0.891352;0.891352;0.891352","-0.14",null,"0.0","0.184;0.055",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","230,0","0","230","0/1","166,36","0.1782","202",null,"chr7:107618411:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1613"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","BTD","chr3:15644883","BTD(G345C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Biotinidase deficiency (BTD deficiency) [MIM:253260]: A juvenile form of multiple carboxylase deficiency, an autosomal recessive disorder of biotin metabolism, characterized by ketoacidosis, hyperammonemia, excretion of abnormal organic acid metabolites, and dermatitis. Biotinidase deficiency is characterized by seizures, hypotonia, skin rash, alopecia, ataxia, hearing loss, and optic atrophy. If untreated, symptoms usually become progressively worse, and coma and death may occur. {ECO:0000269|PubMed:10206677, ECO:0000269|PubMed:9099842, ECO:0000269|PubMed:9654207}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Catalytic release of biotin from biocytin, the product of biotin-dependent carboxylases degradation.; ",{"$nulls":4},"p.Gly345Cys","c.1033G>T","MODERATE","345/545",6,{"$nulls":5},"5","478","420","367","322","444","369","0","0","0","0.2331",{"$nulls":20},"2.193522",".;-2.29;.;.;.;-2.29;-2.29",".;.;2.42;.;.;.;.","1",".;-1.06;.;.;.;-1.06;-1.06",".;.;0.999;.;.;.;.",".;0.044;.;.;.;0.051;0.053",".;0.287;.;.;.;0.274;0.243",{"$nulls":3},"Unknown",-1,"AR","Biotinidase deficiency","Allergy/Immunology/Infectious; Biochemical; Dermatologic; Neurologic; Ophthalmologic",null,"The protein encoded by this gene functions to recycle protein-bound biotin by cleaving biocytin (biotin-epsilon-lysine), a normal product of carboxylase degradation, resulting in regeneration of free biotin. The encoded protein has also been shown to have biotinyl transferase activity. Mutations in this gene are associated with biotinidase deficiency. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Aug 2013].",null,"C0220754","0/0","467,0","0","467","0/1","319,94","0.2276","413",null,"chr3:15644883:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2298"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","BTNL8","chr5:180908756","BTNL8(P74S)",null,null,"topological domain (Extracellular ), domain (Ig-like V-type 1 ), disulfide bond , splice variant (In isoform 4. ), splice variant (In isoform 7. ), splice variant (In isoform 6. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May stimulate primary immune response. Acts on T-cell stimulated sub-optimally through the TCR/CD3 complex stimulating their proliferation and cytokine production. {ECO:0000269|PubMed:24036152}.; ",{"$nulls":4},"p.Pro74Ser","c.220C>T","MODERATE","74/500",2,{"$nulls":5},"5","648","871","495","687","526","749","0","0","0","0.0534",{"$nulls":20},"-1.339847","-0.06","0.49","1","-0.16;0.36;-0.39",".;0.425;.","0.469;0.485;0.437","0.148;0.19;0.096",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","641,0","0","641","0/1","804,49","0.0574","853",null,"chr5:180908756:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0597"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","CAMSAP1","chr9:135866464","CAMSAP1(H220Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19508979, PubMed:21834987, PubMed:24486153, PubMed:24706919, PubMed:24117850). Specifically recognizes growing microtubule minus-ends and stabilizes microtubules (PubMed:24486153, PubMed:24706919). Acts on free microtubule minus-ends that are not capped by microtubule- nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153, PubMed:24706919). In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (- TIP) that dissociates from microtubules after allowing tubulin incorporation (PubMed:24486153, PubMed:24706919). Through interaction with spectrin may regulate neurite outgrowth (PubMed:24117850). {ECO:0000269|PubMed:19508979, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24117850, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:24706919}.; ",{"$nulls":4},"p.His220Tyr","c.658C>T","MODERATE","220/1613",4,{"$nulls":5},"5","273","130","180","94","245","116","0","0","0","0.1552",{"$nulls":20},"3.78689","2.39;2.42","2.52","0.999994;0.999994;1","-2.41;-2.51","0.996;0.998","0.167;0.25","0.292;0.343",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","271,0","0","271","0/1","103,21","0.1694","124",null,"chr9:135866464:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1809"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","CAMSAP1","chr9:135866464","CAMSAP1(H220Y)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Key microtubule-organizing protein that specifically binds the minus-end of non-centrosomal microtubules and regulates their dynamics and organization (PubMed:19508979, PubMed:21834987, PubMed:24486153, PubMed:24706919, PubMed:24117850). Specifically recognizes growing microtubule minus-ends and stabilizes microtubules (PubMed:24486153, PubMed:24706919). Acts on free microtubule minus-ends that are not capped by microtubule- nucleating proteins or other factors and protects microtubule minus-ends from depolymerization (PubMed:24486153, PubMed:24706919). In contrast to CAMSAP2 and CAMSAP3, tracks along the growing tips of minus-end microtubules without significantly affecting the polymerization rate: binds at the very tip of the microtubules minus-end and acts as a minus-end tracking protein (- TIP) that dissociates from microtubules after allowing tubulin incorporation (PubMed:24486153, PubMed:24706919). Through interaction with spectrin may regulate neurite outgrowth (PubMed:24117850). {ECO:0000269|PubMed:19508979, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:24117850, ECO:0000269|PubMed:24486153, ECO:0000269|PubMed:24706919}.; ",{"$nulls":4},"p.His220Tyr","c.658C>T","MODERATE","220/1613",4,{"$nulls":5},"5","273","157","180","104","245","133","0","0","0","0.188",{"$nulls":20},"3.78689","2.39;2.42","2.52","0.999994;0.999994;1","-2.41;-2.51","0.996;0.998","0.167;0.25","0.292;0.343",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","270,0","0","270","0/1","124,30","0.1948","154",null,"chr9:135866464:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1923"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","CHD5","chr1:6121526","CHD5(A1583P)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Defects in CHD5 may be a cause of the development of cancers from epithelial, neural and hematopoietic origin. CHD5 is one of the missing genes in the del(1p36), a deletion which is extremely common in this type of cancers. A decrease of its expression, results in increased susceptibility of cells to Ras- mediated transformation in vitro and in vivo (PubMed:17289567). {ECO:0000269|PubMed:17289567}.; ","FUNCTION: Chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. May specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non- methylated 'Lys-4' of histone H3. Plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys- 27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. Tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. Downstream activated genes may include CDKN2A that positively regulates the p53/TP53 pathway, which in turn, prevents cell proliferation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. {ECO:0000269|PubMed:23948251}.; ",{"$nulls":4},"p.Ala1583Pro","c.4747G>C","MODERATE","1583/1954",32,{"$nulls":5},"5","194","350","142","245","163","297","0","0","0","0.0673",{"$nulls":20},"-0.566477","-2.72","-0.345","1","-0.47","0.004","0.269","0.117",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and gene transcription. This gene is a potential tumor suppressor gene that may play a role in the development of neuroblastoma. [provided by RefSeq, Feb 2012].  ",null,null,"0/0","190,0","0","190","0/1","315,22","0.0653","337",null,"chr1:6121526:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0776"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","CHML","chr1:241635568","CHML(D67N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM in supporting prenylation of Rab3 family. {ECO:0000269|PubMed:12356470, ECO:0000269|PubMed:15186776, ECO:0000269|PubMed:8294464}.; ",{"$nulls":4},"p.Asp67Asn","c.199G>A","MODERATE","67/656",2,{"$nulls":5},"5","492","489","373","351","436","416","0","0","0","0.3389",{"$nulls":20},"1.088873","0.34;.","0.955;.","1;1;0.848843","-1.0;.","0.001;.","0.287;.","0.091;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","480,0","0","480","0/1","303,165","0.3526","468",null,"chr1:241635568:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3561"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","CHML","chr1:241635568","CHML(D67N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM in supporting prenylation of Rab3 family. {ECO:0000269|PubMed:12356470, ECO:0000269|PubMed:15186776, ECO:0000269|PubMed:8294464}.; ",{"$nulls":4},"p.Asp67Asn","c.199G>A","MODERATE","67/656",2,{"$nulls":5},"5","492","451","373","340","436","392","0","0","0","0.3724",{"$nulls":20},"1.088873","0.34;.","0.955;.","1;1;0.848843","-1.0;.","0.001;.","0.287;.","0.091;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","479,0","0","479","0/1","267,169","0.3876","436",null,"chr1:241635568:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3882"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","COL4A6","chrX:108169521","COL4A6(G1239A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS).; DISEASE: Deafness, X-linked, 6 (DFNX6) [MIM:300914]: A non- syndromic form of sensorineural hearing loss with prelingual onset. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:23714752}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.; ","level2",{"$nulls":3},"p.Gly1239Ala","c.3716G>C","MODERATE","1239/1707",38,{"$nulls":5},"5","509","456","347","315","448","405","0","0","0","0.316",{"$nulls":20},"2.757977","-5.75;-5.75;.;-5.75;.;-4.16",".;3.16;.;.;.;.","0.999996","-5.34;-5.34;.;-5.15;.;-5.12","1.0;1.0;.;0.999;.;.","0.0;0.0;.;0.003;.;0.0","0.932;0.958;0.954;0.791;0.778;0.921",{"$nulls":3},"Unknown",-1,"XL","Deafness, X-linked, with cochlear malformation","Audiologic/Otolaryngologic","kCANCER",null,null,"C3806737","0/0","483,0","0","483","0/1","284,142","0.3333","426",null,"chrX:108169521:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3302"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","COL4A6","chrX:108169521","COL4A6(G1239A)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS).; DISEASE: Deafness, X-linked, 6 (DFNX6) [MIM:300914]: A non- syndromic form of sensorineural hearing loss with prelingual onset. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:23714752}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.; ","level2",{"$nulls":3},"p.Gly1239Ala","c.3716G>C","MODERATE","1239/1707",38,{"$nulls":5},"5","509","600","347","418","452","540","0","0","0","0.3537",{"$nulls":20},"2.757977","-5.75;-5.75;.;-5.75;.;-4.16",".;3.16;.;.;.;.","0.999996","-5.34;-5.34;.;-5.15;.;-5.12","1.0;1.0;.;0.999;.;.","0.0;0.0;.;0.003;.;0.0","0.932;0.958;0.954;0.791;0.778;0.921",{"$nulls":3},"Unknown",-1,"XL","Deafness, X-linked, with cochlear malformation","Audiologic/Otolaryngologic","kCANCER",null,null,"C3806737","0/0","485,0","0","485","0/1","368,201","0.3533","569",null,"chrX:108169521:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3541"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","CTSK","chr1:150805907","CTSK(S118C)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Closely involved in osteoclastic bone resorption and may participate partially in the disorder of bone remodeling. Displays potent endoprotease activity against fibrinogen at acid pH. May play an important role in extracellular matrix degradation.; ",{"$nulls":5},"c.353C>G","HIGH",null,4,{"$nulls":5},"4","561","462","406","337","450","390","0","0","0","0.3282",{"$nulls":20},"3.673292","-4.74","3.84;.","0.996764","-3.24;-3.11","0.894;.","0.002;0.001","0.425;.",{"$nulls":3},"Unknown",-1,"AR","Pycnodysostosis","Biochemical; Craniofacial; Musculoskeletal",null,"The protein encoded by this gene is a lysosomal cysteine proteinase involved in bone remodeling and resorption. This protein, which is a member of the peptidase C1 protein family, is predominantly expressed in osteoclasts. However, the encoded protein is also expressed in a significant fraction of human breast cancers, where it could contribute to tumor invasiveness. Mutations in this gene are the cause of pycnodysostosis, an autosomal recessive disease characterized by osteosclerosis and short stature. [provided by RefSeq, Apr 2013].  ",null,"C0238402","0/0","531,0","0","531","0/1","302,137","0.3121","439",null,"chr1:150805907:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3116"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","CTSK","chr1:150805907","CTSK(S118C)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Closely involved in osteoclastic bone resorption and may participate partially in the disorder of bone remodeling. Displays potent endoprotease activity against fibrinogen at acid pH. May play an important role in extracellular matrix degradation.; ",{"$nulls":5},"c.353C>G","HIGH",null,4,{"$nulls":5},"4","561","800","406","565","449","679","0","0","0","0.2784",{"$nulls":20},"3.673292","-4.74","3.84;.","0.996764","-3.24;-3.11","0.894;.","0.002;0.001","0.425;.",{"$nulls":3},"Unknown",-1,"AR","Pycnodysostosis","Biochemical; Craniofacial; Musculoskeletal",null,"The protein encoded by this gene is a lysosomal cysteine proteinase involved in bone remodeling and resorption. This protein, which is a member of the peptidase C1 protein family, is predominantly expressed in osteoclasts. However, the encoded protein is also expressed in a significant fraction of human breast cancers, where it could contribute to tumor invasiveness. Mutations in this gene are the cause of pycnodysostosis, an autosomal recessive disease characterized by osteosclerosis and short stature. [provided by RefSeq, Apr 2013].  ",null,"C0238402","0/0","528,0","0","528","0/1","564,192","0.254","756",null,"chr1:150805907:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2566"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","CUL4B","chrX:120541667","CUL4B(Q478*)",null,null,"helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Mental retardation, X-linked, syndromic, 15 (MRXS15) [MIM:300354]: A syndromic form of X-linked mental retardation characterized by severe intellectual deficit associated with short stature, craniofacial dysmorphism, small testes, muscle wasting in lower legs, kyphosis, joint hyperextensibility, pes cavus, small feet, and abnormalities of the toes. Additional neurologic manifestations include speech delay and impairment, tremor, seizures, gait ataxia, hyperactivity and decreased attention span. {ECO:0000269|PubMed:17236139, ECO:0000269|PubMed:17273978, ECO:0000269|PubMed:19377476, ECO:0000269|PubMed:20002452}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Core component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the E3 ubiquitin-protein ligase complex depends on the variable substrate recognition subunit. CUL4B may act within the complex as a scaffold protein, contributing to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. Plays a role as part of the E3 ubiquitin-protein ligase complex in polyubiquitination of CDT1, histone H2A, histone H3 and histone H4 in response to radiation- induced DNA damage. Targeted to UV damaged chromatin by DDB2 and may be important for DNA repair and DNA replication. Required for ubiquitination of cyclin E, and consequently, normal G1 cell cycle progression. Regulates the mammalian target-of-rapamycin (mTOR) pathway involved in control of cell growth, size and metabolism. Specific CUL4B regulation of the mTORC1-mediated pathway is dependent upon 26S proteasome function and requires interaction between CUL4B and MLST8. {ECO:0000269|PubMed:14578910, ECO:0000269|PubMed:16322693, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:18235224, ECO:0000269|PubMed:18593899, ECO:0000269|PubMed:19801544, ECO:0000269|PubMed:22118460}.; ","gedi",{"$nulls":3},"p.Gln478*","c.1432C>T","HIGH","478/913",12,{"$nulls":5},"5","226","193","150","126","201","176","0","0","0","0.392",{"$nulls":5},"(CUL4B|ENSG00000158290|1|1.00)","(CUL4B|ENSG00000158290|1|1.00)",{"$nulls":13},"7.971482",null,null,"1",{"$nulls":3},"0.905;0.905;0.907",{"$nulls":3},"Unknown",-1,"XL","Mental retardation, X-linked, syndromic 15","Craniofacial; Endocrine; Musculoskeletal; Neurologic",null,"This gene is a member of the cullin family. The encoded protein forms a complex that functions as an E3 ubiquitin ligase and catalyzes the polyubiquitination of specific protein substrates in the cell. The protein interacts with a ring finger protein, and is required for the proteolysis of several regulators of DNA replication including chromatin licensing and DNA replication factor 1 and cyclin E. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].",null,"C1845861","0/0","222,0","0","222","0/1","116,72","0.383","188",null,"chrX:120541667:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4048"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","CUL4B","chrX:120541667","CUL4B(Q478*)",null,null,"helix ",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Mental retardation, X-linked, syndromic, 15 (MRXS15) [MIM:300354]: A syndromic form of X-linked mental retardation characterized by severe intellectual deficit associated with short stature, craniofacial dysmorphism, small testes, muscle wasting in lower legs, kyphosis, joint hyperextensibility, pes cavus, small feet, and abnormalities of the toes. Additional neurologic manifestations include speech delay and impairment, tremor, seizures, gait ataxia, hyperactivity and decreased attention span. {ECO:0000269|PubMed:17236139, ECO:0000269|PubMed:17273978, ECO:0000269|PubMed:19377476, ECO:0000269|PubMed:20002452}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Core component of multiple cullin-RING-based E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the E3 ubiquitin-protein ligase complex depends on the variable substrate recognition subunit. CUL4B may act within the complex as a scaffold protein, contributing to catalysis through positioning of the substrate and the ubiquitin-conjugating enzyme. Plays a role as part of the E3 ubiquitin-protein ligase complex in polyubiquitination of CDT1, histone H2A, histone H3 and histone H4 in response to radiation- induced DNA damage. Targeted to UV damaged chromatin by DDB2 and may be important for DNA repair and DNA replication. Required for ubiquitination of cyclin E, and consequently, normal G1 cell cycle progression. Regulates the mammalian target-of-rapamycin (mTOR) pathway involved in control of cell growth, size and metabolism. Specific CUL4B regulation of the mTORC1-mediated pathway is dependent upon 26S proteasome function and requires interaction between CUL4B and MLST8. {ECO:0000269|PubMed:14578910, ECO:0000269|PubMed:16322693, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:18235224, ECO:0000269|PubMed:18593899, ECO:0000269|PubMed:19801544, ECO:0000269|PubMed:22118460}.; ","gedi",{"$nulls":3},"p.Gln478*","c.1432C>T","HIGH","478/913",12,{"$nulls":5},"5","226","223","150","149","202","206","0","0","0","0.2282",{"$nulls":5},"(CUL4B|ENSG00000158290|1|1.00)","(CUL4B|ENSG00000158290|1|1.00)",{"$nulls":13},"7.971482",null,null,"1",{"$nulls":3},"0.905;0.905;0.907",{"$nulls":3},"Unknown",-1,"XL","Mental retardation, X-linked, syndromic 15","Craniofacial; Endocrine; Musculoskeletal; Neurologic",null,"This gene is a member of the cullin family. The encoded protein forms a complex that functions as an E3 ubiquitin ligase and catalyzes the polyubiquitination of specific protein substrates in the cell. The protein interacts with a ring finger protein, and is required for the proteolysis of several regulators of DNA replication including chromatin licensing and DNA replication factor 1 and cyclin E. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].",null,"C1845861","0/0","222,0","0","222","0/1","169,53","0.2387","222",null,"chrX:120541667:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2282"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","CXorf57","chrX:106612105","CXorf57(E9Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu9Gln","c.25G>C","MODERATE","9/855",1,{"$nulls":5},"5","423","356","325","266","352","309","0","0","0","0.4013",{"$nulls":20},"0.050332","1.03;1.04",null,"1","0.06",null,".;1.0","0.062;0.07",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","412,0","0","412","0/1","208,137","0.3971","345",null,"chrX:106612105:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.406"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","CXorf57","chrX:106612105","CXorf57(E9Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu9Gln","c.25G>C","MODERATE","9/855",1,{"$nulls":5},"5","423","566","325","425","352","491","0","0","0","0.2342",{"$nulls":20},"0.050332","1.03;1.04",null,"1","0.06",null,".;1.0","0.062;0.07",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","418,0","0","418","0/1","433,128","0.2282","561",null,"chrX:106612105:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2376"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","EFHC2","chrX:44242277","EFHC2(S375L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser375Leu","c.1124C>T","MODERATE","375/749",8,{"$nulls":5},"5","268","243","179","177","249","220","0","0","0","0.3091",{"$nulls":20},"3.08727",null,"1.715","0.994573",null,"0.017",null,"0.244",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","269,0","0","269","0/1","162,79","0.3278","241",null,"chrX:44242277:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3277"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","EFHC2","chrX:44242277","EFHC2(S375L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Ser375Leu","c.1124C>T","MODERATE","375/749",8,{"$nulls":5},"5","268","278","179","185","246","248","0","0","0","0.3065",{"$nulls":20},"3.08727",null,"1.715","0.994573",null,"0.017",null,"0.244",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","264,0","0","264","0/1","183,88","0.3247","271",null,"chrX:44242277:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2973"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","EIF4G2","chr11:10799351","EIF4G2(E800Q)",null,null,"domain (W2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Appears to play a role in the switch from cap-dependent to IRES-mediated translation during mitosis, apoptosis and viral infection. Cleaved by some caspases and viral proteases. {ECO:0000269|PubMed:11511540, ECO:0000269|PubMed:11943866, ECO:0000269|PubMed:9032289, ECO:0000269|PubMed:9049310}.; ",{"$nulls":4},"p.Glu800Gln","c.2398G>C","MODERATE","800/907",20,1,{"$nulls":4},"5","588","552","434","405","489","478","0.0017","0.0017","0","0.3556",{"$nulls":20},"2.617628","2.21;2.21;2.21;2.23;.;.",".;.;.;.;1.15;.",null,"-0.56;-0.56;-0.56;-0.56;.;-0.54",".;.;.;.;0.62;.","0.366;0.366;0.366;0.313;.;0.469",{"$nulls":4},"Unknown",-1,{"$nulls":7},"0/0","563,1","0.0018","564","0/1","330,193","0.369","523",null,"chr11:10799351:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3654"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","EIF4G2","chr11:10799351","EIF4G2(E800Q)",null,null,"domain (W2 ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Appears to play a role in the switch from cap-dependent to IRES-mediated translation during mitosis, apoptosis and viral infection. Cleaved by some caspases and viral proteases. {ECO:0000269|PubMed:11511540, ECO:0000269|PubMed:11943866, ECO:0000269|PubMed:9032289, ECO:0000269|PubMed:9049310}.; ",{"$nulls":4},"p.Glu800Gln","c.2398G>C","MODERATE","800/907",20,1,{"$nulls":4},"5","588","611","434","444","486","505","0.0017","0.0017","0","0.2792",{"$nulls":20},"2.617628","2.21;2.21;2.21;2.23;.;.",".;.;.;.;1.15;.",null,"-0.56;-0.56;-0.56;-0.56;.;-0.54",".;.;.;.;0.62;.","0.366;0.366;0.366;0.313;.;0.469",{"$nulls":4},"Unknown",-1,{"$nulls":7},"0/0","563,1","0.0018","564","0/1","419,160","0.2763","579",null,"chr11:10799351:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.268"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","EIF4G3","chr1:20973003","EIF4G3(T331fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Probable component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome. Thought to be a functional homolog of EIF4G1. {ECO:0000269|PubMed:9418880}.; ",{"$nulls":4},"p.Thr331fs","c.991dupA","HIGH","331/1774",8,{"$nulls":5},"4","164","110","122","82","124","116","0","0","0","0.5086",{"$nulls":5},"(EIF4G3|ENSG00000075151|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","146,0","0","146","0/1","36,68","0.6538","104",null,"chr1:20973003:G:GT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.622"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","EIF4G3","chr1:20973003","EIF4G3(T331fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Probable component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome. Thought to be a functional homolog of EIF4G1. {ECO:0000269|PubMed:9418880}.; ",{"$nulls":4},"p.Thr331fs","c.991dupA","HIGH","331/1774",8,{"$nulls":5},"4","164","151","122","95","123","146","0","0","0","0.3836",{"$nulls":5},"(EIF4G3|ENSG00000075151|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":7},"0/0","148,0","0","148","0/1","79,56","0.4148","135",null,"chr1:20973003:G:GT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3579"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ELL","chr19:18461697","ELL(D209N)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Elongation factor component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Elongation factor component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968, PubMed:23932780). Specifically required for stimulating the elongation step of RNA polymerase II- and III-dependent snRNA gene transcription (PubMed:23932780). ELL also plays an early role before its assembly into in the SEC complex by stabilizing RNA polymerase II recruitment/initiation and entry into the pause site. Required to stabilize the pre-initiation complex and early elongation. {ECO:0000269|PubMed:16006523, ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:22195968, ECO:0000269|PubMed:22252557, ECO:0000269|PubMed:23932780, ECO:0000269|PubMed:8596958}.; ","level2",{"$nulls":3},"p.Asp209Asn","c.625G>A","MODERATE","209/621",5,{"$nulls":5},"5","526","642","386","442","455","525","0","0","0","0.219",{"$nulls":20},"4.0758469999999996","1.49;.","3.085;.","0.999996","-3.94;.","0.999;.","0.002;.","0.588;0.641",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","494,0","0","494","0/1","480,134","0.2182","614",null,"chr19:18461697:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2308"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ELL","chr19:18461697","ELL(D209N)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Elongation factor component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Elongation factor component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968, PubMed:23932780). Specifically required for stimulating the elongation step of RNA polymerase II- and III-dependent snRNA gene transcription (PubMed:23932780). ELL also plays an early role before its assembly into in the SEC complex by stabilizing RNA polymerase II recruitment/initiation and entry into the pause site. Required to stabilize the pre-initiation complex and early elongation. {ECO:0000269|PubMed:16006523, ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:22195968, ECO:0000269|PubMed:22252557, ECO:0000269|PubMed:23932780, ECO:0000269|PubMed:8596958}.; ","level2",{"$nulls":3},"p.Asp209Asn","c.625G>A","MODERATE","209/621",5,{"$nulls":5},"5","526","618","386","443","457","529","0","0","0","0.1267",{"$nulls":20},"4.0758469999999996","1.49;.","3.085;.","0.999996","-3.94;.","0.999;.","0.002;.","0.588;0.641",{"$nulls":3},"Unknown",-1,{"$nulls":3},"COSMIC",{"$nulls":3},"0/0","492,0","0","492","0/1","508,68","0.1181","576",null,"chr19:18461697:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1264"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","EML3","chr11:62608633","EML3(H340L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. {ECO:0000250}.; ",{"$nulls":4},"p.His340Leu","c.1019A>T","MODERATE","340/917",9,{"$nulls":5},"5","487","414","362","303","412","352","0","0","0","0.358",{"$nulls":20},"3.772174","1.15;1.15;1.05;1.05;1.05","2.14;.;.;.;2.14","0.998275;0.998275;0.997672;0.998275;0.998275","-3.29;-3.29;-3.35;-3.35;-3.35","0.885;0.915;0.021;0.949;0.93","0.031;0.017;0.03;0.018;0.017","0.723;0.748;0.733;0.78;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","473,0","0","473","0/1","247,138","0.3584","385",null,"chr11:62608633:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3531"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","EML3","chr11:62608633","EML3(H340L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. {ECO:0000250}.; ",{"$nulls":4},"p.His340Leu","c.1019A>T","MODERATE","340/917",9,{"$nulls":5},"5","487","531","362","408","414","446","0","0","0","0.2892",{"$nulls":20},"3.772174","1.15;1.15;1.05;1.05;1.05","2.14;.;.;.;2.14","0.998275;0.998275;0.997672;0.998275;0.998275","-3.29;-3.29;-3.35;-3.35;-3.35","0.885;0.915;0.021;0.949;0.93","0.031;0.017;0.03;0.018;0.017","0.723;0.748;0.733;0.78;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","473,0","0","473","0/1","365,143","0.2815","508",null,"chr11:62608633:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2966"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","EPHA7","chr6:93410741","EPHA7(V198I)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs772940573",0.0009246,null,"FUNCTION: Receptor tyrosine kinase which binds promiscuously GPI- anchored ephrin-A family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Among GPI-anchored ephrin-A ligands, EFNA5 is a cognate/functional ligand for EPHA7 and their interaction regulates brain development modulating cell-cell adhesion and repulsion. Has a repellent activity on axons and is for instance involved in the guidance of corticothalamic axons and in the proper topographic mapping of retinal axons to the colliculus. May also regulate brain development through a caspase(CASP3)-dependent proapoptotic activity. Forward signaling may result in activation of components of the ERK signaling pathway including MAP2K1, MAP2K2, MAPK1 AND MAPK3 which are phosphorylated upon activation of EPHA7. {ECO:0000269|PubMed:17726105}.; ",{"$nulls":5},"c.592G>A","HIGH",null,3,{"$nulls":5},"4","397","206","307","166","330","160","0","0","0","0.6125",{"$nulls":20},"3.528683","3.43","3.155","0.999999;1","-0.73;-0.84","1.0;0.977","0.001","0.609;0.55",{"$nulls":3},"ExAC_EAS_AF",0.0009246,{"$nulls":7},"0/0","386,0","0","386","0/1","84,120","0.5882","204",null,"chr6:93410741:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6145"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","FAM83G","chr17:18988370","FAM83G(F189L)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May regulate the bone morphogenetic proteins (BMP) pathway. {ECO:0000269|PubMed:24554596}.; ",{"$nulls":4},"p.Phe189Leu","c.567C>G","MODERATE","189/823",3,{"$nulls":5},"5","517","393","358","264","479","346","0","0","0","0.3757",{"$nulls":20},"3.728666","3.02","1.555","0.992361;0.992361;0.992361;1;1;1;1;1;1","-2.36","0.991","0.214","0.732;0.73",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","505,0","0","505","0/1","231,144","0.384","375",null,"chr17:18988370:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3977"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","FAM83G","chr17:18988370","FAM83G(F189L)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May regulate the bone morphogenetic proteins (BMP) pathway. {ECO:0000269|PubMed:24554596}.; ",{"$nulls":4},"p.Phe189Leu","c.567C>G","MODERATE","189/823",3,{"$nulls":5},"5","517","429","358","275","479","389","0","0","0","0.3907",{"$nulls":20},"3.728666","3.02","1.555","0.992361;0.992361;0.992361;1;1;1;1;1;1","-2.36","0.991","0.214","0.732;0.73",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","505,0","0","505","0/1","249,160","0.3912","409",null,"chr17:18988370:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.36"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","FCRL1","chr1:157802479","FCRL1(E169Q)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 2 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as an activating coreceptor in B-cells. May function in B-cells activation and differentiation. {ECO:0000269|PubMed:15479727}.; ",{"$nulls":4},"p.Glu169Gln","c.505G>C","MODERATE","169/429",4,{"$nulls":5},"5","492","458","374","347","386","366","0","0","0","0.377",{"$nulls":20},"2.362329","4.01","1.65","0.748515","-1.65;-1.55;-1.55","0.537;1.0;0.569","0.153;0.153;0.152","0.442;0.376;0.375",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","480,0","0","480","0/1","287,158","0.3551","445",null,"chr1:157802479:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3343"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","FCRL1","chr1:157802479","FCRL1(E169Q)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 2 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function as an activating coreceptor in B-cells. May function in B-cells activation and differentiation. {ECO:0000269|PubMed:15479727}.; ",{"$nulls":4},"p.Glu169Gln","c.505G>C","MODERATE","169/429",4,{"$nulls":5},"5","492","581","374","442","387","478","0","0","0","0.431",{"$nulls":20},"2.362329","4.01","1.65","0.748515","-1.65;-1.55;-1.55","0.537;1.0;0.569","0.153;0.153;0.152","0.442;0.376;0.375",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","479,0","0","479","0/1","340,228","0.4014","568",null,"chr1:157802479:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4118"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","FGFR3","chr4:1799443","FGFR3(S100F)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs587778352",8.346e-06,"DISEASE: Achondroplasia (ACH) [MIM:100800]: A frequent form of short-limb dwarfism. It is characterized by a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. ACH is an autosomal dominant disease. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7758520, ECO:0000269|PubMed:7847369, ECO:0000269|PubMed:8078586, ECO:0000269|PubMed:8599935}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Crouzon syndrome with acanthosis nigricans (CAN) [MIM:612247]: Classic Crouzon disease which is caused by mutations in the FGFR2 gene is characterized by craniosynostosis (premature fusion of the skull sutures), and facial hypoplasia. Crouzon syndrome with acanthosis nigricans (a skin disorder characterized by pigmentation anomalies), CAN, is considered to be an independent disorder from classic Crouzon syndrome. CAN is characterized by additional more severe physical manifestation, such as Chiari malformation, hydrocephalus, and atresia or stenosis of the choanas, and is caused by a specific mutation (Ala-391 to Glu) in the transmembrane domain of FGFR3. It is proposed to have an autosomal dominant mode of inheritance. {ECO:0000269|PubMed:17935505, ECO:0000269|PubMed:7493034}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 1 (TD1) [MIM:187600]: A neonatal lethal skeletal dysplasia. Affected individuals manifest severe shortening of the limbs with macrocephaly, narrow thorax, short ribs, and curved femurs. {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10671061, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8589699, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9790257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 2 (TD2) [MIM:187601]: A neonatal lethal skeletal dysplasia causing severe shortening of the limbs, narrow thorax and short ribs. Patients with thanatophoric dysplasia type 2 have straight femurs and cloverleaf skull. {ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8754806}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypochondroplasia (HCH) [MIM:146000]: Autosomal dominant disease and is characterized by disproportionate short stature. It resembles achondroplasia, but with a less severe phenotype. {ECO:0000269|PubMed:10215410, ECO:0000269|PubMed:10777366, ECO:0000269|PubMed:11055896, ECO:0000269|PubMed:12707965, ECO:0000269|PubMed:7670477, ECO:0000269|PubMed:9452043}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. {ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:11314002}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Somatic mutations can constitutively activate FGFR3.; DISEASE: Cervical cancer (CERCA) [MIM:603956]: A malignant neoplasm of the cervix, typically originating from a dysplastic or premalignant lesion previously present at the active squamocolumnar junction. The transformation from mild dysplastic to invasive carcinoma generally occurs slowly within several years, although the rate of this process varies widely. Carcinoma in situ is particularly known to precede invasive cervical cancer in most cases. Cervical cancer is strongly associated with infection by oncogenic types of human papillomavirus. {ECO:0000269|PubMed:10471491}. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Camptodactyly, tall stature, and hearing loss syndrome (CATSHLS) [MIM:610474]: An autosomal dominant syndrome characterized by permanent and irreducible flexion of one or more fingers of the hand and/or feet, tall stature, scoliosis and/or a pectus excavatum, and hearing loss. Affected individuals have developmental delay and/or mental retardation, and several of these have microcephaly. Radiographic findings included tall vertebral bodies with irregular borders and broad femoral metaphyses with long tubular shafts. On audiological exam, each tested member have bilateral sensorineural hearing loss and absent otoacoustic emissions. The hearing loss was congenital or developed in early infancy, progressed variably in early childhood, and range from mild to severe. Computed tomography and magnetic resonance imaging reveal that the brain, middle ear, and inner ear are structurally normal. {ECO:0000269|PubMed:17033969}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:11529856, ECO:0000269|PubMed:9207791}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving FGFR3 is found in multiple myeloma. Translocation t(4;14)(p16.3;q32.3) with the IgH locus.; DISEASE: Lacrimo-auriculo-dento-digital syndrome (LADDS) [MIM:149730]: An autosomal dominant ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. Lacrimo-auriculo-dento-digital syndrome is characterized by aplastic/hypoplastic lacrimal and salivary glands and ducts, cup-shaped ears, hearing loss, hypodontia and enamel hypoplasia, and distal limb segments anomalies. In addition to these cardinal features, facial dysmorphism, malformations of the kidney and respiratory system and abnormal genitalia have been reported. Craniosynostosis and severe syndactyly are not observed. {ECO:0000269|PubMed:16501574}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratinocytic non-epidermolytic nevus (KNEN) [MIM:162900]: Epidermal nevi of the common, non-organoid and non- epidermolytic type are benign skin lesions and may vary in their extent from a single (usually linear) lesion to widespread and systematized involvement. They may be present at birth or develop early during childhood. {ECO:0000269|PubMed:16841094}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Muenke syndrome (MNKS) [MIM:602849]: A condition characterized by premature closure of coronal suture of skull during development (coronal craniosynostosis), which affects the shape of the head and face. It may be uni- or bilateral. When bilateral, it is characterized by a skull with a small antero- posterior diameter (brachycephaly), often with a decrease in the depth of the orbits and hypoplasia of the maxillae. Unilateral closure of the coronal sutures leads to flattening of the orbit on the involved side (plagiocephaly). The intellect is normal. In addition to coronal craniosynostosis some affected individuals show skeletal abnormalities of hands and feet, sensorineural hearing loss, mental retardation and respiratory insufficiency. {ECO:0000269|PubMed:11746040, ECO:0000269|PubMed:9042914, ECO:0000269|PubMed:9950359}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratosis, seborrheic (KERSEB) [MIM:182000]: A common benign skin tumor. Seborrheic keratoses usually begin with the appearance of one or more sharply defined, light brown, flat macules. The lesions may be sparse or numerous. As they initially grow, they develop a velvety to finely verrucous surface, followed by an uneven warty surface with multiple plugged follicles and a dull or lackluster appearance. {ECO:0000269|PubMed:15772091}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:19855393}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Achondroplasia, severe, with developmental delay and acanthosis nigricans (SADDAN) [MIM:616482]: A severe form of achondroplasia associated with developmental delay and acanthosis nigricans. Patients manifest short-limb dwarfism, with a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. Acanthosis nigricans is a skin condition characterized by brown-pigmented, velvety verrucosities in body folds and creases. {ECO:0000269|PubMed:10053006}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation and apoptosis. Plays an essential role in the regulation of chondrocyte differentiation, proliferation and apoptosis, and is required for normal skeleton development. Regulates both osteogenesis and postnatal bone mineralization by osteoblasts. Promotes apoptosis in chondrocytes, but can also promote cancer cell proliferation. Required for normal development of the inner ear. Phosphorylates PLCG1, CBL and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Plays a role in the regulation of vitamin D metabolism. Mutations that lead to constitutive kinase activation or impair normal FGFR3 maturation, internalization and degradation lead to aberrant signaling. Over-expressed or constitutively activated FGFR3 promotes activation of PTPN11/SHP2, STAT1, STAT5A and STAT5B. Secreted isoform 3 retains its capacity to bind FGF1 and FGF2 and hence may interfere with FGF signaling. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:11294897, ECO:0000269|PubMed:11703096, ECO:0000269|PubMed:14534538, ECO:0000269|PubMed:16410555, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17145761, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17509076, ECO:0000269|PubMed:17561467, ECO:0000269|PubMed:19088846, ECO:0000269|PubMed:19286672, ECO:0000269|PubMed:8663044}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","p.Ser100Phe","c.299C>T","MODERATE","100/808",3,{"$nulls":5},"5","301","211","240","159","251","177","0","0","0","0.7119",{"$nulls":20},"3.707909","1.88;1.88;1.88;1.88;.;1.88","2.085;.;2.085;2.085;.;2.085","0.999998;0.999998;0.999998;0.999998;0.968215;0.968215","-2.1;-2.08;-2.1;-1.74;.;-1.74","0.2;0.941;0.723;1.0;.;1.0","0.334;0.027;0.532;0.056;.;0.056","0.609;0.581;0.631;0.625;0.613;0.656",{"$nulls":3},"ExAC_AF",8.346e-06,"AD/AR","Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome; Crouzon syndrome with acanthosis nigricans; Lacrimoauriculodentodigital syndrome (AD); Muenke syndrome","Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Neurologic","COSMIC,dcPGX,kCANCER,kMAPK,vRTK",null,null,"C2677099| C1864852| C1868678| C0005684| C1864436| C2674173| C0153594| C0001080| CN043619| C1300257| C0410529| C1527249| C0302592| C0334082| C0265269","0|0","302,0","0","302","0|1","61,148","0.7081","209",null,"chr4:1799443:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7044"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","FGFR3","chr4:1799443","FGFR3(S100F)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs587778352",8.346e-06,"DISEASE: Achondroplasia (ACH) [MIM:100800]: A frequent form of short-limb dwarfism. It is characterized by a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. ACH is an autosomal dominant disease. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7758520, ECO:0000269|PubMed:7847369, ECO:0000269|PubMed:8078586, ECO:0000269|PubMed:8599935}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Crouzon syndrome with acanthosis nigricans (CAN) [MIM:612247]: Classic Crouzon disease which is caused by mutations in the FGFR2 gene is characterized by craniosynostosis (premature fusion of the skull sutures), and facial hypoplasia. Crouzon syndrome with acanthosis nigricans (a skin disorder characterized by pigmentation anomalies), CAN, is considered to be an independent disorder from classic Crouzon syndrome. CAN is characterized by additional more severe physical manifestation, such as Chiari malformation, hydrocephalus, and atresia or stenosis of the choanas, and is caused by a specific mutation (Ala-391 to Glu) in the transmembrane domain of FGFR3. It is proposed to have an autosomal dominant mode of inheritance. {ECO:0000269|PubMed:17935505, ECO:0000269|PubMed:7493034}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 1 (TD1) [MIM:187600]: A neonatal lethal skeletal dysplasia. Affected individuals manifest severe shortening of the limbs with macrocephaly, narrow thorax, short ribs, and curved femurs. {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10671061, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8589699, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9790257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 2 (TD2) [MIM:187601]: A neonatal lethal skeletal dysplasia causing severe shortening of the limbs, narrow thorax and short ribs. Patients with thanatophoric dysplasia type 2 have straight femurs and cloverleaf skull. {ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8754806}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypochondroplasia (HCH) [MIM:146000]: Autosomal dominant disease and is characterized by disproportionate short stature. It resembles achondroplasia, but with a less severe phenotype. {ECO:0000269|PubMed:10215410, ECO:0000269|PubMed:10777366, ECO:0000269|PubMed:11055896, ECO:0000269|PubMed:12707965, ECO:0000269|PubMed:7670477, ECO:0000269|PubMed:9452043}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. {ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:11314002}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Somatic mutations can constitutively activate FGFR3.; DISEASE: Cervical cancer (CERCA) [MIM:603956]: A malignant neoplasm of the cervix, typically originating from a dysplastic or premalignant lesion previously present at the active squamocolumnar junction. The transformation from mild dysplastic to invasive carcinoma generally occurs slowly within several years, although the rate of this process varies widely. Carcinoma in situ is particularly known to precede invasive cervical cancer in most cases. Cervical cancer is strongly associated with infection by oncogenic types of human papillomavirus. {ECO:0000269|PubMed:10471491}. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Camptodactyly, tall stature, and hearing loss syndrome (CATSHLS) [MIM:610474]: An autosomal dominant syndrome characterized by permanent and irreducible flexion of one or more fingers of the hand and/or feet, tall stature, scoliosis and/or a pectus excavatum, and hearing loss. Affected individuals have developmental delay and/or mental retardation, and several of these have microcephaly. Radiographic findings included tall vertebral bodies with irregular borders and broad femoral metaphyses with long tubular shafts. On audiological exam, each tested member have bilateral sensorineural hearing loss and absent otoacoustic emissions. The hearing loss was congenital or developed in early infancy, progressed variably in early childhood, and range from mild to severe. Computed tomography and magnetic resonance imaging reveal that the brain, middle ear, and inner ear are structurally normal. {ECO:0000269|PubMed:17033969}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:11529856, ECO:0000269|PubMed:9207791}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving FGFR3 is found in multiple myeloma. Translocation t(4;14)(p16.3;q32.3) with the IgH locus.; DISEASE: Lacrimo-auriculo-dento-digital syndrome (LADDS) [MIM:149730]: An autosomal dominant ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. Lacrimo-auriculo-dento-digital syndrome is characterized by aplastic/hypoplastic lacrimal and salivary glands and ducts, cup-shaped ears, hearing loss, hypodontia and enamel hypoplasia, and distal limb segments anomalies. In addition to these cardinal features, facial dysmorphism, malformations of the kidney and respiratory system and abnormal genitalia have been reported. Craniosynostosis and severe syndactyly are not observed. {ECO:0000269|PubMed:16501574}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratinocytic non-epidermolytic nevus (KNEN) [MIM:162900]: Epidermal nevi of the common, non-organoid and non- epidermolytic type are benign skin lesions and may vary in their extent from a single (usually linear) lesion to widespread and systematized involvement. They may be present at birth or develop early during childhood. {ECO:0000269|PubMed:16841094}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Muenke syndrome (MNKS) [MIM:602849]: A condition characterized by premature closure of coronal suture of skull during development (coronal craniosynostosis), which affects the shape of the head and face. It may be uni- or bilateral. When bilateral, it is characterized by a skull with a small antero- posterior diameter (brachycephaly), often with a decrease in the depth of the orbits and hypoplasia of the maxillae. Unilateral closure of the coronal sutures leads to flattening of the orbit on the involved side (plagiocephaly). The intellect is normal. In addition to coronal craniosynostosis some affected individuals show skeletal abnormalities of hands and feet, sensorineural hearing loss, mental retardation and respiratory insufficiency. {ECO:0000269|PubMed:11746040, ECO:0000269|PubMed:9042914, ECO:0000269|PubMed:9950359}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratosis, seborrheic (KERSEB) [MIM:182000]: A common benign skin tumor. Seborrheic keratoses usually begin with the appearance of one or more sharply defined, light brown, flat macules. The lesions may be sparse or numerous. As they initially grow, they develop a velvety to finely verrucous surface, followed by an uneven warty surface with multiple plugged follicles and a dull or lackluster appearance. {ECO:0000269|PubMed:15772091}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:19855393}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Achondroplasia, severe, with developmental delay and acanthosis nigricans (SADDAN) [MIM:616482]: A severe form of achondroplasia associated with developmental delay and acanthosis nigricans. Patients manifest short-limb dwarfism, with a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. Acanthosis nigricans is a skin condition characterized by brown-pigmented, velvety verrucosities in body folds and creases. {ECO:0000269|PubMed:10053006}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation and apoptosis. Plays an essential role in the regulation of chondrocyte differentiation, proliferation and apoptosis, and is required for normal skeleton development. Regulates both osteogenesis and postnatal bone mineralization by osteoblasts. Promotes apoptosis in chondrocytes, but can also promote cancer cell proliferation. Required for normal development of the inner ear. Phosphorylates PLCG1, CBL and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Plays a role in the regulation of vitamin D metabolism. Mutations that lead to constitutive kinase activation or impair normal FGFR3 maturation, internalization and degradation lead to aberrant signaling. Over-expressed or constitutively activated FGFR3 promotes activation of PTPN11/SHP2, STAT1, STAT5A and STAT5B. Secreted isoform 3 retains its capacity to bind FGF1 and FGF2 and hence may interfere with FGF signaling. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:11294897, ECO:0000269|PubMed:11703096, ECO:0000269|PubMed:14534538, ECO:0000269|PubMed:16410555, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17145761, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17509076, ECO:0000269|PubMed:17561467, ECO:0000269|PubMed:19088846, ECO:0000269|PubMed:19286672, ECO:0000269|PubMed:8663044}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","p.Ser100Phe","c.299C>T","MODERATE","100/808",3,{"$nulls":5},"5","301","247","240","187","251","205","0","0","0","0.3317",{"$nulls":20},"3.707909","1.88;1.88;1.88;1.88;.;1.88","2.085;.;2.085;2.085;.;2.085","0.999998;0.999998;0.999998;0.999998;0.968215;0.968215","-2.1;-2.08;-2.1;-1.74;.;-1.74","0.2;0.941;0.723;1.0;.;1.0","0.334;0.027;0.532;0.056;.;0.056","0.609;0.581;0.631;0.625;0.613;0.656",{"$nulls":3},"ExAC_AF",8.346e-06,"AD/AR","Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome; Crouzon syndrome with acanthosis nigricans; Lacrimoauriculodentodigital syndrome (AD); Muenke syndrome","Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Neurologic","COSMIC,dcPGX,kCANCER,kMAPK,vRTK",null,null,"C2677099| C1864852| C1868678| C0005684| C1864436| C2674173| C0153594| C0001080| CN043619| C1300257| C0410529| C1527249| C0302592| C0334082| C0265269","0/0","297,0","0","297","0/1","148,83","0.3593","231",null,"chr4:1799443:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.369"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","FGFR3","chr4:1799455","FGFR3(S104F)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Achondroplasia (ACH) [MIM:100800]: A frequent form of short-limb dwarfism. It is characterized by a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. ACH is an autosomal dominant disease. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7758520, ECO:0000269|PubMed:7847369, ECO:0000269|PubMed:8078586, ECO:0000269|PubMed:8599935}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Crouzon syndrome with acanthosis nigricans (CAN) [MIM:612247]: Classic Crouzon disease which is caused by mutations in the FGFR2 gene is characterized by craniosynostosis (premature fusion of the skull sutures), and facial hypoplasia. Crouzon syndrome with acanthosis nigricans (a skin disorder characterized by pigmentation anomalies), CAN, is considered to be an independent disorder from classic Crouzon syndrome. CAN is characterized by additional more severe physical manifestation, such as Chiari malformation, hydrocephalus, and atresia or stenosis of the choanas, and is caused by a specific mutation (Ala-391 to Glu) in the transmembrane domain of FGFR3. It is proposed to have an autosomal dominant mode of inheritance. {ECO:0000269|PubMed:17935505, ECO:0000269|PubMed:7493034}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 1 (TD1) [MIM:187600]: A neonatal lethal skeletal dysplasia. Affected individuals manifest severe shortening of the limbs with macrocephaly, narrow thorax, short ribs, and curved femurs. {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10671061, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8589699, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9790257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 2 (TD2) [MIM:187601]: A neonatal lethal skeletal dysplasia causing severe shortening of the limbs, narrow thorax and short ribs. Patients with thanatophoric dysplasia type 2 have straight femurs and cloverleaf skull. {ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8754806}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypochondroplasia (HCH) [MIM:146000]: Autosomal dominant disease and is characterized by disproportionate short stature. It resembles achondroplasia, but with a less severe phenotype. {ECO:0000269|PubMed:10215410, ECO:0000269|PubMed:10777366, ECO:0000269|PubMed:11055896, ECO:0000269|PubMed:12707965, ECO:0000269|PubMed:7670477, ECO:0000269|PubMed:9452043}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. {ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:11314002}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Somatic mutations can constitutively activate FGFR3.; DISEASE: Cervical cancer (CERCA) [MIM:603956]: A malignant neoplasm of the cervix, typically originating from a dysplastic or premalignant lesion previously present at the active squamocolumnar junction. The transformation from mild dysplastic to invasive carcinoma generally occurs slowly within several years, although the rate of this process varies widely. Carcinoma in situ is particularly known to precede invasive cervical cancer in most cases. Cervical cancer is strongly associated with infection by oncogenic types of human papillomavirus. {ECO:0000269|PubMed:10471491}. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Camptodactyly, tall stature, and hearing loss syndrome (CATSHLS) [MIM:610474]: An autosomal dominant syndrome characterized by permanent and irreducible flexion of one or more fingers of the hand and/or feet, tall stature, scoliosis and/or a pectus excavatum, and hearing loss. Affected individuals have developmental delay and/or mental retardation, and several of these have microcephaly. Radiographic findings included tall vertebral bodies with irregular borders and broad femoral metaphyses with long tubular shafts. On audiological exam, each tested member have bilateral sensorineural hearing loss and absent otoacoustic emissions. The hearing loss was congenital or developed in early infancy, progressed variably in early childhood, and range from mild to severe. Computed tomography and magnetic resonance imaging reveal that the brain, middle ear, and inner ear are structurally normal. {ECO:0000269|PubMed:17033969}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:11529856, ECO:0000269|PubMed:9207791}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving FGFR3 is found in multiple myeloma. Translocation t(4;14)(p16.3;q32.3) with the IgH locus.; DISEASE: Lacrimo-auriculo-dento-digital syndrome (LADDS) [MIM:149730]: An autosomal dominant ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. Lacrimo-auriculo-dento-digital syndrome is characterized by aplastic/hypoplastic lacrimal and salivary glands and ducts, cup-shaped ears, hearing loss, hypodontia and enamel hypoplasia, and distal limb segments anomalies. In addition to these cardinal features, facial dysmorphism, malformations of the kidney and respiratory system and abnormal genitalia have been reported. Craniosynostosis and severe syndactyly are not observed. {ECO:0000269|PubMed:16501574}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratinocytic non-epidermolytic nevus (KNEN) [MIM:162900]: Epidermal nevi of the common, non-organoid and non- epidermolytic type are benign skin lesions and may vary in their extent from a single (usually linear) lesion to widespread and systematized involvement. They may be present at birth or develop early during childhood. {ECO:0000269|PubMed:16841094}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Muenke syndrome (MNKS) [MIM:602849]: A condition characterized by premature closure of coronal suture of skull during development (coronal craniosynostosis), which affects the shape of the head and face. It may be uni- or bilateral. When bilateral, it is characterized by a skull with a small antero- posterior diameter (brachycephaly), often with a decrease in the depth of the orbits and hypoplasia of the maxillae. Unilateral closure of the coronal sutures leads to flattening of the orbit on the involved side (plagiocephaly). The intellect is normal. In addition to coronal craniosynostosis some affected individuals show skeletal abnormalities of hands and feet, sensorineural hearing loss, mental retardation and respiratory insufficiency. {ECO:0000269|PubMed:11746040, ECO:0000269|PubMed:9042914, ECO:0000269|PubMed:9950359}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratosis, seborrheic (KERSEB) [MIM:182000]: A common benign skin tumor. Seborrheic keratoses usually begin with the appearance of one or more sharply defined, light brown, flat macules. The lesions may be sparse or numerous. As they initially grow, they develop a velvety to finely verrucous surface, followed by an uneven warty surface with multiple plugged follicles and a dull or lackluster appearance. {ECO:0000269|PubMed:15772091}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:19855393}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Achondroplasia, severe, with developmental delay and acanthosis nigricans (SADDAN) [MIM:616482]: A severe form of achondroplasia associated with developmental delay and acanthosis nigricans. Patients manifest short-limb dwarfism, with a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. Acanthosis nigricans is a skin condition characterized by brown-pigmented, velvety verrucosities in body folds and creases. {ECO:0000269|PubMed:10053006}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation and apoptosis. Plays an essential role in the regulation of chondrocyte differentiation, proliferation and apoptosis, and is required for normal skeleton development. Regulates both osteogenesis and postnatal bone mineralization by osteoblasts. Promotes apoptosis in chondrocytes, but can also promote cancer cell proliferation. Required for normal development of the inner ear. Phosphorylates PLCG1, CBL and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Plays a role in the regulation of vitamin D metabolism. Mutations that lead to constitutive kinase activation or impair normal FGFR3 maturation, internalization and degradation lead to aberrant signaling. Over-expressed or constitutively activated FGFR3 promotes activation of PTPN11/SHP2, STAT1, STAT5A and STAT5B. Secreted isoform 3 retains its capacity to bind FGF1 and FGF2 and hence may interfere with FGF signaling. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:11294897, ECO:0000269|PubMed:11703096, ECO:0000269|PubMed:14534538, ECO:0000269|PubMed:16410555, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17145761, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17509076, ECO:0000269|PubMed:17561467, ECO:0000269|PubMed:19088846, ECO:0000269|PubMed:19286672, ECO:0000269|PubMed:8663044}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","p.Ser104Phe","c.311C>T","MODERATE","104/808",3,{"$nulls":5},"5","318","215","250","157","275","191","0","0","0","0.712",{"$nulls":20},"3.102744","1.64;1.64;1.64;1.64;.;1.64","3.365;.;3.365;3.365;.;3.365","0.999927;0.999927;0.999927;0.999927;0.977751;0.977751","-3.94;-3.88;-3.94;-3.37;.;-3.37","0.995;0.999;0.968;1.0;.;1.0","0.001;0.0;0.0;0.006;.;0.006","0.399;0.367;0.381;0.429;0.372;0.418",{"$nulls":3},"Unknown",-1,"AD/AR","Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome; Crouzon syndrome with acanthosis nigricans; Lacrimoauriculodentodigital syndrome (AD); Muenke syndrome","Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Neurologic","COSMIC,dcPGX,kCANCER,kMAPK,vRTK",null,null,"C2677099| C1864852| C1868678| C0005684| C1864436| C2674173| C0153594| C0001080| CN043619| C1300257| C0410529| C1527249| C0302592| C0334082| C0265269","0|0","316,0","0","316","0|1","61,149","0.7095","210",null,"chr4:1799455:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7134"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","FGFR3","chr4:1799455","FGFR3(S104F)",null,null,"topological domain (Extracellular ), domain (Ig-like C2-type 1 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Achondroplasia (ACH) [MIM:100800]: A frequent form of short-limb dwarfism. It is characterized by a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. ACH is an autosomal dominant disease. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7758520, ECO:0000269|PubMed:7847369, ECO:0000269|PubMed:8078586, ECO:0000269|PubMed:8599935}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Crouzon syndrome with acanthosis nigricans (CAN) [MIM:612247]: Classic Crouzon disease which is caused by mutations in the FGFR2 gene is characterized by craniosynostosis (premature fusion of the skull sutures), and facial hypoplasia. Crouzon syndrome with acanthosis nigricans (a skin disorder characterized by pigmentation anomalies), CAN, is considered to be an independent disorder from classic Crouzon syndrome. CAN is characterized by additional more severe physical manifestation, such as Chiari malformation, hydrocephalus, and atresia or stenosis of the choanas, and is caused by a specific mutation (Ala-391 to Glu) in the transmembrane domain of FGFR3. It is proposed to have an autosomal dominant mode of inheritance. {ECO:0000269|PubMed:17935505, ECO:0000269|PubMed:7493034}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 1 (TD1) [MIM:187600]: A neonatal lethal skeletal dysplasia. Affected individuals manifest severe shortening of the limbs with macrocephaly, narrow thorax, short ribs, and curved femurs. {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10671061, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8589699, ECO:0000269|PubMed:8845844, ECO:0000269|PubMed:9790257}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thanatophoric dysplasia 2 (TD2) [MIM:187601]: A neonatal lethal skeletal dysplasia causing severe shortening of the limbs, narrow thorax and short ribs. Patients with thanatophoric dysplasia type 2 have straight femurs and cloverleaf skull. {ECO:0000269|PubMed:12297284, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8754806}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hypochondroplasia (HCH) [MIM:146000]: Autosomal dominant disease and is characterized by disproportionate short stature. It resembles achondroplasia, but with a less severe phenotype. {ECO:0000269|PubMed:10215410, ECO:0000269|PubMed:10777366, ECO:0000269|PubMed:11055896, ECO:0000269|PubMed:12707965, ECO:0000269|PubMed:7670477, ECO:0000269|PubMed:9452043}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. {ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:11314002}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Somatic mutations can constitutively activate FGFR3.; DISEASE: Cervical cancer (CERCA) [MIM:603956]: A malignant neoplasm of the cervix, typically originating from a dysplastic or premalignant lesion previously present at the active squamocolumnar junction. The transformation from mild dysplastic to invasive carcinoma generally occurs slowly within several years, although the rate of this process varies widely. Carcinoma in situ is particularly known to precede invasive cervical cancer in most cases. Cervical cancer is strongly associated with infection by oncogenic types of human papillomavirus. {ECO:0000269|PubMed:10471491}. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Camptodactyly, tall stature, and hearing loss syndrome (CATSHLS) [MIM:610474]: An autosomal dominant syndrome characterized by permanent and irreducible flexion of one or more fingers of the hand and/or feet, tall stature, scoliosis and/or a pectus excavatum, and hearing loss. Affected individuals have developmental delay and/or mental retardation, and several of these have microcephaly. Radiographic findings included tall vertebral bodies with irregular borders and broad femoral metaphyses with long tubular shafts. On audiological exam, each tested member have bilateral sensorineural hearing loss and absent otoacoustic emissions. The hearing loss was congenital or developed in early infancy, progressed variably in early childhood, and range from mild to severe. Computed tomography and magnetic resonance imaging reveal that the brain, middle ear, and inner ear are structurally normal. {ECO:0000269|PubMed:17033969}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:11529856, ECO:0000269|PubMed:9207791}. Note=The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving FGFR3 is found in multiple myeloma. Translocation t(4;14)(p16.3;q32.3) with the IgH locus.; DISEASE: Lacrimo-auriculo-dento-digital syndrome (LADDS) [MIM:149730]: An autosomal dominant ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. Lacrimo-auriculo-dento-digital syndrome is characterized by aplastic/hypoplastic lacrimal and salivary glands and ducts, cup-shaped ears, hearing loss, hypodontia and enamel hypoplasia, and distal limb segments anomalies. In addition to these cardinal features, facial dysmorphism, malformations of the kidney and respiratory system and abnormal genitalia have been reported. Craniosynostosis and severe syndactyly are not observed. {ECO:0000269|PubMed:16501574}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratinocytic non-epidermolytic nevus (KNEN) [MIM:162900]: Epidermal nevi of the common, non-organoid and non- epidermolytic type are benign skin lesions and may vary in their extent from a single (usually linear) lesion to widespread and systematized involvement. They may be present at birth or develop early during childhood. {ECO:0000269|PubMed:16841094}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Muenke syndrome (MNKS) [MIM:602849]: A condition characterized by premature closure of coronal suture of skull during development (coronal craniosynostosis), which affects the shape of the head and face. It may be uni- or bilateral. When bilateral, it is characterized by a skull with a small antero- posterior diameter (brachycephaly), often with a decrease in the depth of the orbits and hypoplasia of the maxillae. Unilateral closure of the coronal sutures leads to flattening of the orbit on the involved side (plagiocephaly). The intellect is normal. In addition to coronal craniosynostosis some affected individuals show skeletal abnormalities of hands and feet, sensorineural hearing loss, mental retardation and respiratory insufficiency. {ECO:0000269|PubMed:11746040, ECO:0000269|PubMed:9042914, ECO:0000269|PubMed:9950359}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratosis, seborrheic (KERSEB) [MIM:182000]: A common benign skin tumor. Seborrheic keratoses usually begin with the appearance of one or more sharply defined, light brown, flat macules. The lesions may be sparse or numerous. As they initially grow, they develop a velvety to finely verrucous surface, followed by an uneven warty surface with multiple plugged follicles and a dull or lackluster appearance. {ECO:0000269|PubMed:15772091}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:19855393}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Achondroplasia, severe, with developmental delay and acanthosis nigricans (SADDAN) [MIM:616482]: A severe form of achondroplasia associated with developmental delay and acanthosis nigricans. Patients manifest short-limb dwarfism, with a long, narrow trunk, short extremities, particularly in the proximal (rhizomelic) segments, a large head with frontal bossing, hypoplasia of the midface and a trident configuration of the hands. Acanthosis nigricans is a skin condition characterized by brown-pigmented, velvety verrucosities in body folds and creases. {ECO:0000269|PubMed:10053006}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation and apoptosis. Plays an essential role in the regulation of chondrocyte differentiation, proliferation and apoptosis, and is required for normal skeleton development. Regulates both osteogenesis and postnatal bone mineralization by osteoblasts. Promotes apoptosis in chondrocytes, but can also promote cancer cell proliferation. Required for normal development of the inner ear. Phosphorylates PLCG1, CBL and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Plays a role in the regulation of vitamin D metabolism. Mutations that lead to constitutive kinase activation or impair normal FGFR3 maturation, internalization and degradation lead to aberrant signaling. Over-expressed or constitutively activated FGFR3 promotes activation of PTPN11/SHP2, STAT1, STAT5A and STAT5B. Secreted isoform 3 retains its capacity to bind FGF1 and FGF2 and hence may interfere with FGF signaling. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:11294897, ECO:0000269|PubMed:11703096, ECO:0000269|PubMed:14534538, ECO:0000269|PubMed:16410555, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17145761, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17509076, ECO:0000269|PubMed:17561467, ECO:0000269|PubMed:19088846, ECO:0000269|PubMed:19286672, ECO:0000269|PubMed:8663044}.; ","gedi|foundationOne|illumina|ion|level2","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","[ \"Bortezomib\" , \"Pazopanib\" , \"Ponatinib\" , \"Vemurafenib\"]","p.Ser104Phe","c.311C>T","MODERATE","104/808",3,{"$nulls":5},"5","318","255","250","188","275","211","0","0","0","0.2796",{"$nulls":20},"3.102744","1.64;1.64;1.64;1.64;.;1.64","3.365;.;3.365;3.365;.;3.365","0.999927;0.999927;0.999927;0.999927;0.977751;0.977751","-3.94;-3.88;-3.94;-3.37;.;-3.37","0.995;0.999;0.968;1.0;.;1.0","0.001;0.0;0.0;0.006;.;0.006","0.399;0.367;0.381;0.429;0.372;0.418",{"$nulls":3},"Unknown",-1,"AD/AR","Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome; Crouzon syndrome with acanthosis nigricans; Lacrimoauriculodentodigital syndrome (AD); Muenke syndrome","Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Musculoskeletal; Neurologic","COSMIC,dcPGX,kCANCER,kMAPK,vRTK",null,null,"C2677099| C1864852| C1868678| C0005684| C1864436| C2674173| C0153594| C0001080| CN043619| C1300257| C0410529| C1527249| C0302592| C0334082| C0265269","0/0","311,0","0","311","0/1","154,83","0.3502","237",null,"chr4:1799455:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3511"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","FRYL","chr4:48543935","FRYL(S1822P)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Plays a key role in maintaining the integrity of polarized cell extensions during morphogenesis, regulates the actin cytoskeleton and plays a key role in patterning sensory neuron dendritic fields by promoting avoidance between homologous dendrites as well as by limiting dendritic branching (By similarity). May function as a transcriptional activator. {ECO:0000250, ECO:0000269|PubMed:16061630}.; ",{"$nulls":4},"p.Ser1822Pro","c.5464T>C","MODERATE","1822/3013",44,{"$nulls":5},"4","276","247","195","167","248","212","0","0","0","0.0613",{"$nulls":20},"4.184918","1.63","2.775","1","-3.72","0.998","0.002","0.899;0.901",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","266,0","0","266","0/1","224,15","0.0628","239",null,"chr4:48543935:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0778"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","FSIP2","chr2:185802392","FSIP2(F4451L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Phe4451Leu","c.13353C>G","MODERATE","4451/6996",17,{"$nulls":5},"5","459","335","358","267","398","286","0","0","0","0.3462",{"$nulls":20},"-0.027214","0.72","1.955","1","-3.98",null,"0.243","0.051",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748403","0/0","455,0","0","455","0/1","219,114","0.3423","333",null,"chr2:185802392:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3446"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","FSIP2","chr2:185802392","FSIP2(F4451L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Phe4451Leu","c.13353C>G","MODERATE","4451/6996",17,{"$nulls":5},"5","459","446","358","366","400","376","0","0","0","0.3032",{"$nulls":20},"-0.027214","0.72","1.955","1","-3.98",null,"0.243","0.051",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748403","0/0","452,0","0","452","0/1","303,132","0.3034","435",null,"chr2:185802392:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2923"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GAB4","chr22:16991948","GAB4(E135Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu135Gln","c.403G>C","MODERATE","135/574",2,{"$nulls":5},"5","547","510","401","371","463","448","0","0","0","0.3616",{"$nulls":20},"3.091261","2.42;.","2.065;.","0.999998","-2.31;.","0.999;.","0.005;.","0.492;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","513,0","0","513","0/1","309,167","0.3508","476",null,"chr22:16991948:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.345"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","GAB4","chr22:16991948","GAB4(E135Q)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Glu135Gln","c.403G>C","MODERATE","135/574",2,{"$nulls":5},"5","547","622","401","444","463","556","0","0","0","0.277",{"$nulls":20},"3.091261","2.42;.","2.065;.","0.999998","-2.31;.","0.999;.","0.005;.","0.492;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","516,0","0","516","0/1","416,155","0.2715","571",null,"chr22:16991948:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2725"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GAPDH","chr12:6537988","GAPDH(L310L)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D- glyceroyl phosphate. Component of the GAIT (gamma interferon- activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. {ECO:0000250, ECO:0000269|PubMed:11724794, ECO:0000269|PubMed:23071094, ECO:0000269|PubMed:3170585}.; ",{"$nulls":5},"c.930C>G","HIGH",null,8,{"$nulls":5},"5","393","539","324","430","305","429","0","0","0","0.296",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","381,0","0","381","0/1","377,146","0.2792","523",null,"chr12:6537988:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2628"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","GAPDH","chr12:6537988","GAPDH(L310L)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D- glyceroyl phosphate. Component of the GAIT (gamma interferon- activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. {ECO:0000250, ECO:0000269|PubMed:11724794, ECO:0000269|PubMed:23071094, ECO:0000269|PubMed:3170585}.; ",{"$nulls":5},"c.930C>G","HIGH",null,8,{"$nulls":5},"5","393","590","324","476","305","484","0","0","0","0.2562",{"$nulls":31},"Unknown",-1,{"$nulls":7},"0/0","381,0","0","381","0/1","444,137","0.2358","581",null,"chr12:6537988:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2416"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GIGYF1","chr7:100686320","GIGYF1(G270*)",null,null,"compositionally biased region (Poly-Gly )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May act cooperatively with GRB10 to regulate tyrosine kinase receptor signaling. May increase IGF1 receptor phosphorylation under IGF1 stimulation as well as phosphorylation of IRS1 and SHC1 (By similarity). {ECO:0000250, ECO:0000269|PubMed:12771153}.; ",{"$nulls":4},"p.Gly270*","c.808G>T","HIGH","270/1035",8,{"$nulls":5},"4",null,null,"96","96","118","114",null,null,"0","0.3158",{"$nulls":5},"(GIGYF1|ENSG00000146830|1|1.00)","(GIGYF1|ENSG00000146830|1|1.00)",{"$nulls":13},"7.015427",null,null,"1",{"$nulls":3},"0.307;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","123,0","0","126","0/1","83,49","0.3712","134",null,"chr7:100686320:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4062"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","GIGYF1","chr7:100686320","GIGYF1(G270*)",null,null,"compositionally biased region (Poly-Gly )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May act cooperatively with GRB10 to regulate tyrosine kinase receptor signaling. May increase IGF1 receptor phosphorylation under IGF1 stimulation as well as phosphorylation of IRS1 and SHC1 (By similarity). {ECO:0000250, ECO:0000269|PubMed:12771153}.; ",{"$nulls":4},"p.Gly270*","c.808G>T","HIGH","270/1035",8,{"$nulls":5},"5","126","151","96","111","117","127","0","0","0","0.1969",{"$nulls":5},"(GIGYF1|ENSG00000146830|1|1.00)","(GIGYF1|ENSG00000146830|1|1.00)",{"$nulls":13},"7.015427",null,null,"1",{"$nulls":3},"0.307;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","104,0","0","104","0/1","95,29","0.2339","124",null,"chr7:100686320:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2072"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GNB4","chr3:179415017","GNB4(V100M)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signaling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein- effector interaction.; ",{"$nulls":4},"p.Val100Met","c.298G>A","MODERATE","100/340",6,{"$nulls":5},"4","187","203","127","143",null,null,"0","0",{"$nulls":22},"3.615506","-0.79","4.075","1","-2.57","1.0","0.0","0.891;0.892",{"$nulls":3},"Unknown",-1,"AD","Charcot-Marie-Tooth disease, dominant intermediate F","Neurologic",{"$nulls":3},"C3554654","0/0","186,0","0","186","0/1","189,11","0.055","200",null,"chr3:179415017:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0629"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GPALPP1","chr13:45004403","GPALPP1(E63K)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs374387240",1.5000000000000002E-5,{"$nulls":6},"p.Glu63Lys","c.187G>A","MODERATE","63/340",2,{"$nulls":5},"5","221","105","150","73","205","97","0","0","0","0.5258",{"$nulls":20},"2.796086",null,"0.835;.","0.99679","-1.26;.","0.007;.","0.069;.","0.372;0.362",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,{"$nulls":7},"0/0","219,0","0","219","0/1","49,55","0.5288","104",null,"chr13:45004403:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4932"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","GPALPP1","chr13:45004403","GPALPP1(E63K)",null,null,"splice variant (In isoform 3. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense","rs374387240",1.5000000000000002E-5,{"$nulls":6},"p.Glu63Lys","c.187G>A","MODERATE","63/340",2,{"$nulls":5},"5","221","174","150","128","208","154","0","0","0","0.4675",{"$nulls":20},"2.796086",null,"0.835;.","0.99679","-1.26;.","0.007;.","0.069;.","0.372;0.362",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,{"$nulls":7},"0/0","219,0","0","219","0/1","87,84","0.4912","171",null,"chr13:45004403:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5078"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GPRASP1","chrX:102656211","GPRASP1(R766S)",null,null,"compositionally biased region (Glu-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Modulates lysosomal sorting and functional down- regulation of a variety of G-protein coupled receptors. Targets receptors for degradation in lysosomes via its interaction with BECN2. {ECO:0000269|PubMed:12142540, ECO:0000269|PubMed:15452121, ECO:0000269|PubMed:23954414}.; ",{"$nulls":4},"p.Arg766Ser","c.2298A>C","MODERATE","766/1395",5,{"$nulls":5},"5","394","327","299","236","337","277","0","0","0","0.065",{"$nulls":20},"1.772735","2.47","2.3","1","-1.04","0.02","0.002","0.127;0.107;0.134;0.109",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","395,0","0","395","0/1","306,19","0.0585","325",null,"chrX:102656211:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0551"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GRM5","chr11:89047505","GRM5(E123G)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: G-protein coupled receptor for glutamate. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Signaling activates a phosphatidylinositol-calcium second messenger system and generates a calcium-activated chloride current. Plays an important role in the regulation of synaptic plasticity and the modulation of the neural network activity. {ECO:0000269|PubMed:25042998, ECO:0000269|PubMed:7908515}.; ",{"$nulls":4},"p.Glu123Gly","c.368A>G","MODERATE","123/1212",1,{"$nulls":5},"4","508","2395","372","1764","446","2077","0","0","0","0.0708",{"$nulls":20},"3.416671","-2.4;-2.4;-2.4;-3.37","1.15;1.15;1.15;.","0.999992","-1.9;-1.9;-1.9;-2.68","0.002;0.002;1.0;0.498","0.412;0.412;0.317;0.47","0.395;0.401;0.457;0.361",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","490,0","0","490","0/1","2107,168","0.0738","2275",null,"chr11:89047505:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0765"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","GRM5","chr11:89047505","GRM5(E123G)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: G-protein coupled receptor for glutamate. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors. Signaling activates a phosphatidylinositol-calcium second messenger system and generates a calcium-activated chloride current. Plays an important role in the regulation of synaptic plasticity and the modulation of the neural network activity. {ECO:0000269|PubMed:25042998, ECO:0000269|PubMed:7908515}.; ",{"$nulls":4},"p.Glu123Gly","c.368A>G","MODERATE","123/1212",1,{"$nulls":5},"3",null,null,"372","1640","446","1882",null,null,"0","0.0515",{"$nulls":20},"3.416671","-2.4;-2.4;-2.4;-3.37","1.15;1.15;1.15;.","0.999992","-1.9;-1.9;-1.9;-2.68","0.002;0.002;1.0;0.498","0.412;0.412;0.317;0.47","0.395;0.401;0.457;0.361",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","508,0","0","508","0/1","2093,111","0.0504","2204",null,"chr11:89047505:T:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0506"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","GTF2IRD1","chr7:74538141","GTF2IRD1(D504V)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Note=GTF2IRD1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of GTF2IRD1 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease.; ","FUNCTION: May be a transcription regulator involved in cell-cycle progression and skeletal muscle differentiation. May repress GTF2I transcriptional functions, by preventing its nuclear residency, or by inhibiting its transcriptional activation. May contribute to slow-twitch fiber type specificity during myogenesis and in regenerating muscles. Binds troponin I slow-muscle fiber enhancer (USE B1). Binds specifically and with high affinity to the EFG sequences derived from the early enhancer of HOXC8 (By similarity). {ECO:0000250, ECO:0000269|PubMed:11438732}.; ",{"$nulls":4},"p.Asp504Val","c.1511A>T","MODERATE","504/976",12,{"$nulls":5},"5","449","461","384","403","330","302","0","0","0","0.4536",{"$nulls":20},"3.905099","1.52","0.49;.;0.49;.","0.999999","-3.63","0.129;.;0.204;0.051","0.012;0.042;0.013;0.117","0.574;0.394;0.333;0.339",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","444,0","0","444","0/1","273,182","0.4","455",null,"chr7:74538141:A:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4045"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","HGF","chr7:81705744","HGF(V589V)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Deafness, autosomal recessive, 39 (DFNB39) [MIM:608265]: A form of profound prelingual sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:19576567}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Potent mitogen for mature parenchymal hepatocyte cells, seems to be a hepatotrophic factor, and acts as a growth factor for a broad spectrum of tissues and cell types. Activating ligand for the receptor tyrosine kinase MET by binding to it and promoting its dimerization. {ECO:0000269|PubMed:15167892, ECO:0000269|PubMed:20624990}.; ","gedi|foundationOne|level2",{"$nulls":4},"c.1767C>T","HIGH",null,16,{"$nulls":5},"5","283","290","188","191","245","246","0","0","0","0.3862",{"$nulls":31},"Unknown",-1,"AR","Deafness, autosomal recessive 39","Audiologic/Otolaryngologic","kCANCER",null,null,"C1842342","0/0","279,0","0","279","0/1","170,114","0.4014","284",null,"chr7:81705744:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3874"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","HGF","chr7:81705744","HGF(V589V)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Deafness, autosomal recessive, 39 (DFNB39) [MIM:608265]: A form of profound prelingual sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:19576567}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Potent mitogen for mature parenchymal hepatocyte cells, seems to be a hepatotrophic factor, and acts as a growth factor for a broad spectrum of tissues and cell types. Activating ligand for the receptor tyrosine kinase MET by binding to it and promoting its dimerization. {ECO:0000269|PubMed:15167892, ECO:0000269|PubMed:20624990}.; ","gedi|foundationOne|level2",{"$nulls":4},"c.1767C>T","HIGH",null,16,{"$nulls":5},"5","283","249","188","162","246","222","0","0","0","0.1622",{"$nulls":31},"Unknown",-1,"AR","Deafness, autosomal recessive 39","Audiologic/Otolaryngologic","kCANCER",null,null,"C1842342","0/0","279,0","0","279","0/1","202,41","0.1687","243",null,"chr7:81705744:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1667"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","HMCN1","chr1:186189763","HMCN1(R5598Q)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs748032823",2.6968716289104636E-4,null,"FUNCTION: Promotes cleavage furrow maturation during cytokinesis in preimplantation embryos. May play a role in the architecture of adhesive and flexible epithelial cell junctions. May play a role during myocardial remodeling by imparting an effect on cardiac fibroblast migration. {ECO:0000250|UniProtKB:D3YXG0}.; ",{"$nulls":4},"p.Arg5598Gln","c.16793G>A","MODERATE","5598/5635",107,1,{"$nulls":4},"5","393","364","294","267","353","314","0","0","0","0.3599",{"$nulls":20},"1.734005","-0.02","-0.09","0.998139;0.994056","-0.12","0.003","0.336","0.073",{"$nulls":3},"TWINSUK_AF",2.6968716289104636E-4,{"$nulls":6},"C1864205","0/0","387,0","0","387","0/1","232,123","0.3465","355",null,"chr1:186189763:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3483"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","HMCN1","chr1:186189763","HMCN1(R5598Q)",null,null,"splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense","rs748032823",2.6968716289104636E-4,null,"FUNCTION: Promotes cleavage furrow maturation during cytokinesis in preimplantation embryos. May play a role in the architecture of adhesive and flexible epithelial cell junctions. May play a role during myocardial remodeling by imparting an effect on cardiac fibroblast migration. {ECO:0000250|UniProtKB:D3YXG0}.; ",{"$nulls":4},"p.Arg5598Gln","c.16793G>A","MODERATE","5598/5635",107,1,{"$nulls":4},"5","393","444","294","333","352","374","0","0","0","0.1417",{"$nulls":20},"1.734005","-0.02","-0.09","0.998139;0.994056","-0.12","0.003","0.336","0.073",{"$nulls":3},"TWINSUK_AF",2.6968716289104636E-4,{"$nulls":6},"C1864205","0/0","387,0","0","387","0/1","378,60","0.137","438",null,"chr1:186189763:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1441"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ID2","chr2:8682871","ID2(N127fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. Implicated in regulating a variety of cellular processes, including cellular growth, senescence, differentiation, apoptosis, angiogenesis, and neoplastic transformation. Inhibits skeletal muscle and cardiac myocyte differentiation. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Restricts the CLOCK and ARNTL/BMAL1 localization to the cytoplasm. Plays a role in both the input and output pathways of the circadian clock: in the input component, is involved in modulating the magnitude of photic entrainment and in the output component, contributes to the regulation of a variety of liver clock-controlled genes involved in lipid metabolism. {ECO:0000269|PubMed:20861012}.; ","level2",{"$nulls":3},"p.Asn127fs","c.380dupA","HIGH","127/134",4,{"$nulls":5},"5","308","297","214","196","222","216","0","0","0","0.2963",{"$nulls":5},"(ID2|ENSG00000115738|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"kTGF_BETA",{"$nulls":3},"0/0","272,0","0","272","0/1","182,88","0.3259","270",null,"chr2:8682871:C:CA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3112"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ID2","chr2:8682871","ID2(N127fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. Implicated in regulating a variety of cellular processes, including cellular growth, senescence, differentiation, apoptosis, angiogenesis, and neoplastic transformation. Inhibits skeletal muscle and cardiac myocyte differentiation. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Restricts the CLOCK and ARNTL/BMAL1 localization to the cytoplasm. Plays a role in both the input and output pathways of the circadian clock: in the input component, is involved in modulating the magnitude of photic entrainment and in the output component, contributes to the regulation of a variety of liver clock-controlled genes involved in lipid metabolism. {ECO:0000269|PubMed:20861012}.; ","level2",{"$nulls":3},"p.Asn127fs","c.380dupA","HIGH","127/134",4,{"$nulls":5},"5","308","338","214","231","221","254","0","0","0","0.2441",{"$nulls":5},"(ID2|ENSG00000115738|1|1.00)",{"$nulls":25},"Unknown",-1,{"$nulls":3},"kTGF_BETA",{"$nulls":3},"0/0","272,0","0","272","0/1","228,77","0.2525","305",null,"chr2:8682871:C:CA",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2554"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","IGFN1","chr1:201211930","IGFN1(G2346V)",{"$nulls":6},255,"PASS","Missense","rs763007047",0.000518,{"$nulls":6},"p.Gly2346Val","c.7037G>T","MODERATE","2346/3708",12,{"$nulls":5},"5","333","322","285","281","233","237","0","0","0","0.0928",{"$nulls":20},"1.096438","-0.23",null,"0.999999;1;0.999999","-1.9",null,"0.002","0.072",{"$nulls":3},"ExAC_NFE_AF",0.000518,{"$nulls":7},"0/0","331,0","0","331","0/1","286,29","0.0921","315",null,"chr1:201211930:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0996"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","IMMP2L","chr7:110963532","IMMP2L(K91N)",{"$nulls":3},"active-site:sequence_similarity_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense","rs777413647",1.5320000000000002E-5,null,"FUNCTION: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO. {ECO:0000269|PubMed:15814844}.; ","mitocarta",{"$nulls":3},"p.Lys91Asn","c.273G>C","MODERATE","91/175",5,{"$nulls":5},"5","211","153","145","110","186","131","0","0","0","0.313",{"$nulls":20},"3.267695",null,"4.535;4.535;4.535;.;4.535","0.999999;0.999999;0.999999;0.999219;1;0.999999;1","-4.5;-4.5;-4.5;-4.83;-3.96","0.999;0.999;0.999;.;0.999","0.0;0.0;0.0;0.0;0.002","0.968;0.968;0.968;0.967;0.974",{"$nulls":3},"ExAC_NFE_AF",1.5320000000000002E-5,{"$nulls":7},"0/0","207,0","0","207","0/1","103,48","0.3179","151",null,"chr7:110963532:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3091"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","IMMP2L","chr7:110963532","IMMP2L(K91N)",{"$nulls":3},"active-site:sequence_similarity_evidence_used_in_manual_assertion","LOW",null,255,"PASS","Missense","rs777413647",1.5320000000000002E-5,null,"FUNCTION: Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space. Known to process the nuclear encoded protein DIABLO. {ECO:0000269|PubMed:15814844}.; ","mitocarta",{"$nulls":3},"p.Lys91Asn","c.273G>C","MODERATE","91/175",5,{"$nulls":5},"5","211","183","145","122","187","160","0","0","0","0.0938",{"$nulls":20},"3.267695",null,"4.535;4.535;4.535;.;4.535","0.999999;0.999999;0.999999;0.999219;1;0.999999;1","-4.5;-4.5;-4.5;-4.83;-3.96","0.999;0.999;0.999;.;0.999","0.0;0.0;0.0;0.0;0.002","0.968;0.968;0.968;0.967;0.974",{"$nulls":3},"ExAC_NFE_AF",1.5320000000000002E-5,{"$nulls":7},"0/0","210,0","0","210","0/1","158,17","0.0971","175",null,"chr7:110963532:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0984"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","INTS2","chr17:61867923","INTS2(E1119K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.; ",{"$nulls":4},"p.Glu1119Lys","c.3355G>A","MODERATE","1119/1204",24,{"$nulls":5},"5","168","145","118","102","148","131","0","0","0","0.313",{"$nulls":20},"3.424613",".;0.83;.;0.83","1.495;1.495;.;.","1",".;-2.63;.;.","0.728;0.728;.;.",".;0.037;.;.","0.455;0.459;.;0.461",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","167,0","0","167","0/1","96,44","0.3143","140",null,"chr17:61867923:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3039"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","INTS2","chr17:61867923","INTS2(E1119K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (Probable). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:23904267, ECO:0000305|PubMed:16239144}.; ",{"$nulls":4},"p.Glu1119Lys","c.3355G>A","MODERATE","1119/1204",24,{"$nulls":5},"5","168","147","118","106","150","130","0","0","0","0.1769",{"$nulls":20},"3.424613",".;0.83;.;0.83","1.495;1.495;.;.","1",".;-2.63;.;.","0.728;0.728;.;.",".;0.037;.;.","0.455;0.459;.;0.461",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","168,0","0","168","0/1","117,28","0.1931","145",null,"chr17:61867923:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1981"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ITIH5","chr10:7576689","ITIH5(T581N)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May act as a tumor suppressor.; ",{"$nulls":4},"p.Thr581Asn","c.1742C>A","MODERATE","581/942",10,{"$nulls":5},"4","549","535","408","409","448","438","0","0","0","0.379",{"$nulls":20},"2.8383089999999997","0.12;.;0.12",null,"0.996079;0.997635;0.996079;0.996079","-3.94;.;-3.94",".;.;1.0","0.003;.;0.003","0.51;0.491;0.502",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","516,1","0.0019","517","0/1","327,186","0.3626","513",null,"chr10:7576689:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3619"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","JAK3","chr19:17830182","JAK3(P1045T)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Severe combined immunodeficiency autosomal recessive T- cell-negative/B-cell-positive/NK-cell-negative (T(-)B(+)NK(-) SCID) [MIM:600802]: A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. {ECO:0000269|PubMed:10982185, ECO:0000269|PubMed:14615376, ECO:0000269|PubMed:7659163, ECO:0000269|PubMed:9354668, ECO:0000269|PubMed:9753072}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Non-receptor tyrosine kinase involved in various processes such as cell growth, development, or differentiation. Mediates essential signaling events in both innate and adaptive immunity and plays a crucial role in hematopoiesis during T-cells development. In the cytoplasm, plays a pivotal role in signal transduction via its association with type I receptors sharing the common subunit gamma such as IL2R, IL4R, IL7R, IL9R, IL15R and IL21R. Following ligand binding to cell surface receptors, phosphorylates specific tyrosine residues on the cytoplasmic tails of the receptor, creating docking sites for STATs proteins. Subsequently, phosphorylates the STATs proteins once they are recruited to the receptor. Phosphorylated STATs then form homodimer or heterodimers and translocate to the nucleus to activate gene transcription. For example, upon IL2R activation by IL2, JAK1 and JAK3 molecules bind to IL2R beta (IL2RB) and gamma chain (IL2RG) subunits inducing the tyrosine phosphorylation of both receptor subunits on their cytoplasmic domain. Then, STAT5A AND STAT5B are recruited, phosphorylated and activated by JAK1 and JAK3. Once activated, dimerized STAT5 translocates to the nucleus and promotes the transcription of specific target genes in a cytokine-specific fashion. {ECO:0000269|PubMed:11909529, ECO:0000269|PubMed:20440074, ECO:0000269|PubMed:7662955, ECO:0000269|PubMed:8022485}.; ","gedi|foundationOne|illumina|ion|level2",{"$nulls":3},"p.Pro1045Thr","c.3133C>A","MODERATE","1045/1124",23,{"$nulls":5},"5","185","219","142","148","164","193","0","0","0","0.2642",{"$nulls":20},"1.063704","-1.09;-1.09;-1.08","1.125","0.999954","-1.26","0.005;0.005;0.011","1.0","0.237;0.235;0.144",{"$nulls":3},"Unknown",-1,"AR","Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, natural killer cell-negative ","Allergy/Immunology/Infectious","COSMIC,kJAK_STAT","The protein encoded by this gene is a member of the Janus kinase (JAK) family of tyrosine kinases involved in cytokine receptor-mediated intracellular signal transduction. It is predominantly expressed in immune cells and transduces a signal in response to its activation via tyrosine phosphorylation by interleukin receptors. Mutations in this gene are associated with autosomal SCID (severe combined immunodeficiency disease). [provided by RefSeq, Jul 2008].  ",null,"C1833275","0/0","179,0","0","179","0/1","155,56","0.2654","211",null,"chr19:17830182:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.277"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","KCNT1","chr9:135765690","KCNT1(P423S)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Epileptic encephalopathy, early infantile, 14 (EIEE14) [MIM:614959]: A rare epileptic encephalopathy of infancy that combines pharmacoresistant seizures with developmental delay. This severe neurologic disorder is characterized by onset in the first 6 months of life of refractory focal seizures and arrest of psychomotor development. Ictal EEG shows discharges that arise randomly from various areas of both hemispheres and migrate from one brain region to another. {ECO:0000269|PubMed:23086397, ECO:0000269|PubMed:23708187, ECO:0000269|PubMed:24029078, ECO:0000269|PubMed:24463883, ECO:0000269|PubMed:26993267, ECO:0000269|PubMed:27864847}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epilepsy, nocturnal frontal lobe, 5 (ENFL5) [MIM:615005]: An autosomal dominant focal epilepsy syndrome characterized by childhood onset of clusters of motor seizures during sleep. Some patients may develop behavioral or psychiatric manifestations and/or intellectual disability. The phenotype is more severe than observed in other genetic forms of nocturnal frontal lobe epilepsy. {ECO:0000269|PubMed:23086396}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Outwardly rectifying potassium channel subunit that may coassemble with other Slo-type channel subunits. Activated by high intracellular sodium or chloride levels. Activated upon stimulation of G-protein coupled receptors, such as CHRM1 and GRIA1. May be regulated by calcium in the absence of sodium ions (in vitro) (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro423Ser","c.1267C>T","MODERATE","423/1256",13,1,{"$nulls":4},"4","786","1060","516","693","605","787","0","0","0","0.0572",{"$nulls":20},"4.00704",".;.;-0.39;.;.;1.71;.;.;.;.",".;.;.;.;.;.;.;.;2.7;.","1",".;.;-7.61;-7.6;.;-7.23;.;.;-7.61;-7.61",".;.;.;.;.;.;.;.;0.865;.",".;.;0.056;0.058;.;0.047;.;.;0.051;0.052","0.826;0.881;0.815;0.808;0.892;0.837;0.884;0.824;0.805;0.885",{"$nulls":3},"Unknown",-1,"AD","Epilepsy, nocturnal frontal lobe, 5; Early infantile epileptic encephalopathy 14","Neurologic",{"$nulls":3},"C3554306| C3554195","0/0","756,0","0","756","0/1","947,63","0.0624","1010",null,"chr9:135765690:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0592"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","KIF2B","chr17:53823548","KIF2B(A172V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Plus end-directed microtubule-dependent motor required for spindle assembly and chromosome movement. Has microtubule depolymerization activity (PubMed:17538014). Plays a role in chromosome congression (PubMed:23891108). {ECO:0000269|PubMed:17538014, ECO:0000269|PubMed:23891108}.; ",{"$nulls":4},"p.Ala172Val","c.515C>T","MODERATE","172/673",1,{"$nulls":5},"5","294","247","239","206","266","222","0","0","0","0.2117",{"$nulls":20},"1.844142","-0.81","2.685","0.986827","-0.85","0.749","0.196","0.298",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","289,0","0","289","0/1","192,52","0.2131","244",null,"chr17:53823548:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2184"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","KLC4","chr6:43063082","KLC4(E160K)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu160Lys","c.478G>A","MODERATE","160/637",3,{"$nulls":5},"5","235","107","178","74","213","90","0","0","0","0.5667",{"$nulls":20},"4.289395","0.77;0.12;0.77;0.77;0.77;0.77;0.77","3.4;.;.;3.4;.;3.4;3.4","1","-3.03;-3.56;-3.55;-3.62;-3.03;-3.03;-3.03","0.997;.;.;.;0.996;0.997;0.997","0.001;0.002;0.001;0.001;0.001;0.001;0.001","0.783;.;.;0.756;0.785;0.783;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","223,0","0","223","0/1","41,63","0.6058","104",null,"chr6:43063082:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5811"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","KLC4","chr6:43063082","KLC4(E160K)",null,null,"splice variant (In isoform 5. ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu160Lys","c.478G>A","MODERATE","160/637",3,{"$nulls":5},"5","235","139","178","104","214","127","0","0","0","0.5512",{"$nulls":20},"4.289395","0.77;0.12;0.77;0.77;0.77;0.77;0.77","3.4;.;.;3.4;.;3.4;3.4","1","-3.03;-3.56;-3.55;-3.62;-3.03;-3.03;-3.03","0.997;.;.;.;0.996;0.997;0.997","0.001;0.002;0.001;0.001;0.001;0.001;0.001","0.783;.;.;0.756;0.785;0.783;0.788",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","233,0","0","233","0/1","63,77","0.55","140",null,"chr6:43063082:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5288"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","KLC4","chr6:43070808","KLC4(I384M)",null,null,"repeat (TPR 6 ), splice variant (In isoform 2. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ile384Met","c.1152C>G","MODERATE","384/637",8,{"$nulls":5},"5","332","206","218","137","307","184","0","0","0","0.6576",{"$nulls":20},"2.762835","-3.63","2.325;.;.;2.325;2.325","0.999999","-2.86;-2.82;-2.86;-2.86;-2.86","0.188;.;0.322;0.188;0.188","0.01;0.029;0.037;0.01;0.01","0.88;0.9;0.879;0.878;0.902",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","322,0","0","322","0/1","73,133","0.6456","206",null,"chr6:43070808:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6131"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","KLC4","chr6:43070808","KLC4(I384M)",null,null,"repeat (TPR 6 ), splice variant (In isoform 2. ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Ile384Met","c.1152C>G","MODERATE","384/637",8,{"$nulls":5},"5","332","267","218","189","306","240","0","0","0","0.4542",{"$nulls":20},"2.762835","-3.63","2.325;.;.;2.325;2.325","0.999999","-2.86;-2.82;-2.86;-2.86;-2.86","0.188;.;0.322;0.188;0.188","0.01;0.029;0.037;0.01;0.01","0.88;0.9;0.879;0.878;0.902",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","326,0","0","326","0/1","139,125","0.4735","264",null,"chr6:43070808:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.455"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","LARP6","chr15:70832546","LARP6(Q328*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1215568273",-1,null,"FUNCTION: Regulates the coordinated translation of type I collagen alpha-1 and alpha-2 mRNAs, CO1A1 and CO1A2. Stabilizes mRNAs through high-affinity binding of a stem-loop structure in their 5' UTR. This regulation requires VIM and MYH10 filaments, and the helicase DHX9. {ECO:0000269|PubMed:20603131, ECO:0000269|PubMed:21746880, ECO:0000269|PubMed:22190748}.; ",{"$nulls":4},"p.Gln328*","c.982C>T","HIGH","328/491",3,{"$nulls":5},"4","775","1166","572","834","670","994","0","0","0","0.3813",{"$nulls":20},"7.961032",null,null,"1",{"$nulls":3},"0.352",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","752,0","0","752","0/1","685,433","0.3873","1118",null,"chr15:70832546:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3681"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","LARP6","chr15:70832546","LARP6(Q328*)",{"$nulls":6},255,"PASS","Loss Of Function","rs1215568273",-1,null,"FUNCTION: Regulates the coordinated translation of type I collagen alpha-1 and alpha-2 mRNAs, CO1A1 and CO1A2. Stabilizes mRNAs through high-affinity binding of a stem-loop structure in their 5' UTR. This regulation requires VIM and MYH10 filaments, and the helicase DHX9. {ECO:0000269|PubMed:20603131, ECO:0000269|PubMed:21746880, ECO:0000269|PubMed:22190748}.; ",{"$nulls":4},"p.Gln328*","c.982C>T","HIGH","328/491",3,{"$nulls":5},"4","775","981","572","753","665","839","0","0","0","0.4005",{"$nulls":20},"7.961032",null,null,"1",{"$nulls":3},"0.352",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","746,0","0","746","0/1","566,363","0.3907","929",null,"chr15:70832546:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3944"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MALRD1","chr10:19209477","MALRD1(S930R)",null,null,"topological domain (Vesicular ), domain (MAM 5 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Enhances production and/or transport of FGF19 and thus has a role in regulation of bile acid synthesis. {ECO:0000269|PubMed:23747249}.; ",{"$nulls":4},"p.Ser930Arg","c.2788A>C","MODERATE","930/2156",18,{"$nulls":5},"4","742","580","510","397","679","536","0","0","0","0.209",{"$nulls":20},"4.076478",".;3.93",null,"0.992359",".;-3.15",null,".;0.012","0.784;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","699,0","0","699","0/1","426,121","0.2212","547",null,"chr10:19209477:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2141"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MALRD1","chr10:19352135","MALRD1(E1427Q)",null,null,"topological domain (Vesicular ), domain (MAM 7 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Enhances production and/or transport of FGF19 and thus has a role in regulation of bile acid synthesis. {ECO:0000269|PubMed:23747249}.; ",{"$nulls":4},"p.Glu1427Gln","c.4279G>C","MODERATE","1427/2156",26,{"$nulls":5},"5","476","354","337","255","389","302","0","0","0","0.2682",{"$nulls":20},"1.725031",".;4.39",null,"0.924942",".;-1.61",null,".;0.173","0.073;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","456,0","0","456","0/1","238,93","0.281","331",null,"chr10:19352135:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2588"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MAP3K15","chrX:19431572","MAP3K15(Q344H)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function in a signal transduction pathway that is activated by various cell stresses and leads to apoptosis. {ECO:0000269|PubMed:20362554}.; ",{"$nulls":4},"p.Gln344His","c.1032G>C","MODERATE","344/1313",7,{"$nulls":5},"5","446","438","301","288","403","401","0","0","0","0.3416",{"$nulls":20},"0.613113","2.87","0.455","1;0.999392;0.999392","-2.26",null,"0.06","0.215",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","429,0","0","429","0/1","275,155","0.3605","430",null,"chrX:19431572:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3576"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MAP3K15","chrX:19431572","MAP3K15(Q344H)",null,null,"splice variant (In isoform 2. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: May function in a signal transduction pathway that is activated by various cell stresses and leads to apoptosis. {ECO:0000269|PubMed:20362554}.; ",{"$nulls":4},"p.Gln344His","c.1032G>C","MODERATE","344/1313",7,{"$nulls":5},"5","446","459","301","309","400","418","0","0","0","0.2919",{"$nulls":20},"0.613113","2.87","0.455","1;0.999392;0.999392","-2.26",null,"0.06","0.215",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","425,0","0","425","0/1","316,131","0.2931","447",null,"chrX:19431572:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2945"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MMP16","chr8:88116581","MMP16(G337R)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs141858403",0.000992063492063492,null,"FUNCTION: Endopeptidase that degrades various components of the extracellular matrix, such as collagen type III and fibronectin. Activates progelatinase A. Involved in the matrix remodeling of blood vessels. Isoform short cleaves fibronectin and also collagen type III, but at lower rate. It has no effect on type I, II, IV and V collagen. However, upon interaction with CSPG4, it may be involved in degradation and invasion of type I collagen by melanoma cells. {ECO:0000269|PubMed:11278606}.; ",{"$nulls":4},"p.Gly337Arg","c.1009G>A","MODERATE","337/607",6,2,{"$nulls":4},"5","547","530","395","381","463","458","0","0","0","0.3275",{"$nulls":20},"2.711649","3.11","1.04","0.999999","-0.97","0.203","0.157","0.389",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":4},"Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The encoded protein activates MMP2 by cleavage. This gene was once referred to as MT-MMP2, but was renamed as MT-MMP3 or MMP16. [provided by RefSeq, Oct 2010].  ",null,null,"0/0","537,1","0.0019","538","0/1","345,173","0.334","518",null,"chr8:88116581:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3202"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MMP16","chr8:88116581","MMP16(G337R)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs141858403",0.000992063492063492,null,"FUNCTION: Endopeptidase that degrades various components of the extracellular matrix, such as collagen type III and fibronectin. Activates progelatinase A. Involved in the matrix remodeling of blood vessels. Isoform short cleaves fibronectin and also collagen type III, but at lower rate. It has no effect on type I, II, IV and V collagen. However, upon interaction with CSPG4, it may be involved in degradation and invasion of type I collagen by melanoma cells. {ECO:0000269|PubMed:11278606}.; ",{"$nulls":4},"p.Gly337Arg","c.1009G>A","MODERATE","337/607",6,2,{"$nulls":4},"5","547","647","395","479","465","540","0","0","0","0.2463",{"$nulls":20},"2.711649","3.11","1.04","0.999999","-0.97","0.203","0.157","0.389",{"$nulls":3},"1000Gp3_EAS_AF",0.000992063492063492,{"$nulls":4},"Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The encoded protein activates MMP2 by cleavage. This gene was once referred to as MT-MMP2, but was renamed as MT-MMP3 or MMP16. [provided by RefSeq, Oct 2010].  ",null,null,"0/0","518,1","0.0019","519","0/1","452,151","0.2504","603",null,"chr8:88116581:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2422"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MMP27","chr11:102693961","MMP27(V380I)",null,null,"repeat (Hemopexin 3 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs202071510",1.73E-3,null,"FUNCTION: Matrix metalloproteinases degrade protein components of the extracellular matrix such as fibronectin, laminin, gelatins and/or collagens. {ECO:0000250}.; ",{"$nulls":4},"p.Val380Ile","c.1138G>A","MODERATE","380/513",8,{"$nulls":5},"4","320","1102","256","873","232","844","0","0","0","0.0581",{"$nulls":20},"0.536682","4.21","1.32","0.999984","-0.45","0.006","0.113","0.202",{"$nulls":3},"ExAC_AMR_AF",1.73E-3,{"$nulls":4},"Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","300,0","0","300","0/1","1001,60","0.0566","1061",null,"chr11:102693961:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0584"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MMP27","chr11:102693961","MMP27(V380I)",null,null,"repeat (Hemopexin 3 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense","rs202071510",1.73E-3,null,"FUNCTION: Matrix metalloproteinases degrade protein components of the extracellular matrix such as fibronectin, laminin, gelatins and/or collagens. {ECO:0000250}.; ",{"$nulls":4},"p.Val380Ile","c.1138G>A","MODERATE","380/513",8,{"$nulls":5},"4","320","983","256","787","233","747","0","0","0","0.1084",{"$nulls":20},"0.536682","4.21","1.32","0.999984","-0.45","0.006","0.113","0.202",{"$nulls":3},"ExAC_AMR_AF",1.73E-3,{"$nulls":4},"Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","297,1","0.0034","298","0/1","859,83","0.0881","942",null,"chr11:102693961:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0928"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MOGS","chr2:74461886","MOGS(E635*)",null,null,"topological domain (Lumenal )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Type IIb congenital disorder of glycosylation (CDGIIb) [MIM:606056]: Characterized by marked generalized hypotonia and hypomotility of the neonate, dysmorphic features, including a prominent occiput, short palpebral fissures, retrognathia, high arched palate, generalized edema, and hypoplastic genitalia. Symptoms of the infant included hepatomegaly, hypoventilation, feeding problems and seizures. The clinical course was progressive and the infant did not survive more than a few months. {ECO:0000269|PubMed:10788335}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cleaves the distal alpha 1,2-linked glucose residue from the Glc(3)Man(9)GlcNAc(2) oligosaccharide precursor in a highly specific manner.; ",{"$nulls":4},"p.Glu635*","c.1903G>T","HIGH","635/837",4,{"$nulls":5},"5","256","205","200","176","228","177","0","0","0","0.3842",{"$nulls":20},"6.910412",null,null,"1;1;0.999601",{"$nulls":3},".;0.045;.;.;0.045",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type IIb","Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Hematologic; Musculoskeletal; Neurologic",{"$nulls":3},"C1853736","0/0","253,0","0","253","0/1","124,77","0.3831","201",null,"chr2:74461886:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3693"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MOGS","chr2:74461886","MOGS(E635*)",null,null,"topological domain (Lumenal )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Type IIb congenital disorder of glycosylation (CDGIIb) [MIM:606056]: Characterized by marked generalized hypotonia and hypomotility of the neonate, dysmorphic features, including a prominent occiput, short palpebral fissures, retrognathia, high arched palate, generalized edema, and hypoplastic genitalia. Symptoms of the infant included hepatomegaly, hypoventilation, feeding problems and seizures. The clinical course was progressive and the infant did not survive more than a few months. {ECO:0000269|PubMed:10788335}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Cleaves the distal alpha 1,2-linked glucose residue from the Glc(3)Man(9)GlcNAc(2) oligosaccharide precursor in a highly specific manner.; ",{"$nulls":4},"p.Glu635*","c.1903G>T","HIGH","635/837",4,{"$nulls":5},"5","256","218","200","182","226","187","0","0","0","0.3316",{"$nulls":20},"6.910412",null,null,"1;1;0.999601",{"$nulls":3},".;0.045;.;.;0.045",{"$nulls":3},"Unknown",-1,"AR","Congenital disorder of glycosylation, type IIb","Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Hematologic; Musculoskeletal; Neurologic",{"$nulls":3},"C1853736","0/0","254,0","0","254","0/1","145,69","0.3224","214",null,"chr2:74461886:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3407"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MOS","chr8:56113284","MOS(Q233H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"level2",{"$nulls":3},"p.Gln233His","c.699G>C","MODERATE","233/346",1,{"$nulls":5},"5","571","516","429","395","501","474","0","0","0","0.4008",{"$nulls":20},"1.060489","-0.22","0.91","1","-0.71","0.007","0.098","0.048",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","560,0","0","560","0/1","304,203","0.4004","507",null,"chr8:56113284:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3873"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MOS","chr8:56113284","MOS(Q233H)",{"$nulls":6},255,"PASS","Missense",null,-1,null,null,"level2",{"$nulls":3},"p.Gln233His","c.699G>C","MODERATE","233/346",1,{"$nulls":5},"5","571","510","429","388","502","446","0","0","0","0.1659",{"$nulls":20},"1.060489","-0.22","0.91","1","-0.71","0.007","0.098","0.048",{"$nulls":3},"Unknown",-1,{"$nulls":3},"kMAPK",{"$nulls":3},"0/0","561,0","0","561","0/1","413,84","0.169","497",null,"chr8:56113284:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1727"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MRPL39","chr21:25606590","MRPL39(L47V)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Leu47Val","c.139C>G","MODERATE","47/353",2,{"$nulls":5},"4","479","221","320","145","441","188","0","0","0","0.4681",{"$nulls":20},"1.865837","0.94","1.6;1.6;.","0.996078","-1.75","0.017;0.018;.","0.092;0.074;0.091","0.233;0.234;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","472,0","0","472","0/1","111,106","0.4885","217",null,"chr21:25606590:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4828"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","MRPL39","chr21:25606590","MRPL39(L47V)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,null,"mitocarta",{"$nulls":3},"p.Leu47Val","c.139C>G","MODERATE","47/353",2,{"$nulls":5},"4","479","323","320","203","444","273","0","0","0","0.4212",{"$nulls":20},"1.865837","0.94","1.6;1.6;.","0.996078","-1.75","0.017;0.018;.","0.092;0.074;0.091","0.233;0.234;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","472,0","0","472","0/1","173,146","0.4577","319",null,"chr21:25606590:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4335"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MXRA7","chr17:76685123","MXRA7(G193E)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gly193Glu","c.578G>A","MODERATE","193/213",2,{"$nulls":5},"5","221","222","169","160","188","181","0","0","0","0.0939",{"$nulls":20},"3.338459","-1.43","2.33;2.33;2.33;.","0.999152;0.999152;0.999152;0.999152;1;1;1","-4.52;-4.18;-4.08;.","1.0;1.0;1.0;.","0.003;0.028;0.025;.","0.702;0.591;0.629;0.468",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","206,0","0","206","0/1","184,16","0.08","200",null,"chr17:76685123:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.075"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","MYD88","chr3:38138692","MYD88(P11S)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: MYD88 deficiency (MYD88D) [MIM:612260]: Patients suffer from autosomal recessive, life-threatening, often recurrent pyogenic bacterial infections, including invasive pneumococcal disease, and die between 1 and 11 months of age. Surviving patients are otherwise healthy, with normal resistance to other microbes, and their clinical status improved with age. {ECO:0000269|PubMed:18669862, ECO:0000269|PubMed:19506249, ECO:0000269|PubMed:21057262, ECO:0000269|PubMed:24316379}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in MYD88 are frequently found in many hematological malignancies, such as activated B-cell type diffuse large B-cell lymphoma (ABC-DLBCL), Waldenstroem's macroglobulinemia, cutaneous diffuse large B cell lymphoma (CBCL) and primary central nervous system lymphoma (PCNSL). {ECO:0000269|PubMed:21179087, ECO:0000269|PubMed:22931316}.; ","FUNCTION: Adapter protein involved in the Toll-like receptor and IL-1 receptor signaling pathway in the innate immune response (PubMed:15361868, PubMed:18292575). Acts via IRAK1, IRAK2, IRF7 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response (PubMed:15361868, PubMed:24316379, PubMed:19506249). Increases IL-8 transcription (PubMed:9013863). Involved in IL-18-mediated signaling pathway. Activates IRF1 resulting in its rapid migration into the nucleus to mediate an efficient induction of IFN-beta, NOS2/INOS, and IL12A genes. MyD88-mediated signaling in intestinal epithelial cells is crucial for maintenance of gut homeostasis and controls the expression of the antimicrobial lectin REG3G in the small intestine (By similarity). {ECO:0000250|UniProtKB:P22366, ECO:0000269|PubMed:15361868, ECO:0000269|PubMed:18292575, ECO:0000269|PubMed:19506249, ECO:0000269|PubMed:24316379, ECO:0000269|PubMed:9013863}.; ","gedi|foundationOne|level2",{"$nulls":3},"p.Pro11Ser","c.31C>T","MODERATE","11/317",1,{"$nulls":5},"5","479","248","363","193","367","208","0","0","0","0.6394",{"$nulls":20},"-0.691055","2.97;.;.;3.04;.",null,"1","-0.01;.;0.19;-0.26;.",null,"0.506;.;0.355;0.045;.","0.126;.;0.156;.;.",{"$nulls":3},"Unknown",-1,"AR","MYD88 deficiency","Allergy/Immunology/Infectious","COSMIC,kAPOPTOSIS",null,null,"C1835192| C2677092","0/0","453,0","0","453","0/1","85,153","0.6429","238",null,"chr3:38138692:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6269"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","NBEA","chr13:35606501","NBEA(D2459N)",null,null,"domain (BEACH )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the membrane. May anchor the kinase to cytoskeletal and/or organelle-associated proteins (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp2459Asn","c.7375G>A","MODERATE","2459/2947",48,{"$nulls":5},"5","277","115","180","77","236","99","0","0","0","0.4949",{"$nulls":20},"3.670262","-0.05;.;.;-0.05;-0.05;-0.05","1.375;.;.;.;.;.","1","-4.28;.;.;-4.26;-4.9;-4.77","0.001;.;.;0.004;.;0.709","0.111;.;.;0.111;0.154;0.08","0.381;0.392;0.36;0.392;0.468;0.443",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like membrane recruitment of a highly similar protein in mouse suggest an involvement in neuronal post-Golgi membrane traffic. Mutations in this gene may be associated with a form of autism. This gene and its expression are frequently disrupted in patients with multiple myeloma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants may exist, but their full-length nature has not been determined.[provided by RefSeq, Feb 2011].",null,null,"0/0","266,0","0","266","0/1","57,52","0.4771","109",null,"chr13:35606501:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5065"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","NBEA","chr13:35606501","NBEA(D2459N)",null,null,"domain (BEACH )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the membrane. May anchor the kinase to cytoskeletal and/or organelle-associated proteins (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Asp2459Asn","c.7375G>A","MODERATE","2459/2947",48,{"$nulls":5},"5","277","165","180","111","238","139","0","0","0","0.4388",{"$nulls":20},"3.670262","-0.05;.;.;-0.05;-0.05;-0.05","1.375;.;.;.;.;.","1","-4.28;.;.;-4.26;-4.9;-4.77","0.001;.;.;0.004;.;0.709","0.111;.;.;0.111;0.154;0.08","0.381;0.392;0.36;0.392;0.468;0.443",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like membrane recruitment of a highly similar protein in mouse suggest an involvement in neuronal post-Golgi membrane traffic. Mutations in this gene may be associated with a form of autism. This gene and its expression are frequently disrupted in patients with multiple myeloma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants may exist, but their full-length nature has not been determined.[provided by RefSeq, Feb 2011].",null,null,"0/0","266,0","0","266","0/1","86,73","0.4591","159",null,"chr13:35606501:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4505"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","NDUFA11","chr19:5903690","NDUFA11(R7C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Mitochondrial complex I deficiency (MT-C1D) [MIM:252010]: A disorder of the mitochondrial respiratory chain that causes a wide range of clinical manifestations from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. {ECO:0000269|PubMed:18306244}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.; ","mito100|mitocarta",{"$nulls":3},"p.Arg7Cys","c.19C>T","MODERATE","7/228",1,1,{"$nulls":4},"5","520","634","347","417","472","573","0","0","0","0.2269",{"$nulls":20},"2.97779",null,"0.695;.;0.695","1;1;1;0.999904","-1.62;.;-2.11",".;.;0.431","0.001;.;0.018","0.184;0.149;0.115",{"$nulls":3},"Unknown",-1,"AR","Mitochondrial complex I deficiency","Biochemical; Cardiovascular; Gastrointestinal; Neurologic; Ophthalmologic",{"$nulls":3},"C4748777","0/0","492,0","0","492","0/1","453,141","0.2374","594",null,"chr19:5903690:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2326"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","NDUFA11","chr19:5903690","NDUFA11(R7C)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Mitochondrial complex I deficiency (MT-C1D) [MIM:252010]: A disorder of the mitochondrial respiratory chain that causes a wide range of clinical manifestations from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. {ECO:0000269|PubMed:18306244}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.; ","mito100|mitocarta",{"$nulls":3},"p.Arg7Cys","c.19C>T","MODERATE","7/228",1,1,{"$nulls":4},"5","520","596","347","392","472","535","0","0","0","0.1701",{"$nulls":20},"2.97779",null,"0.695;.;0.695","1;1;1;0.999904","-1.62;.;-2.11",".;.;0.431","0.001;.;0.018","0.184;0.149;0.115",{"$nulls":3},"Unknown",-1,"AR","Mitochondrial complex I deficiency","Biochemical; Cardiovascular; Gastrointestinal; Neurologic; Ophthalmologic",{"$nulls":3},"C4748777","0/0","492,0","0","492","0/1","466,99","0.1752","565",null,"chr19:5903690:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.176"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","NFIX","chr19:13078622","NFIX(S322F)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,"DISEASE: Sotos syndrome 2 (SOTOS2) [MIM:614753]: A form of Sotos syndrome, a childhood overgrowth syndrome characterized by prenatal and postnatal overgrowth, developmental delay, mental retardation, advanced bone age, and abnormal craniofacial morphology. SOTOS2 patients have macrocephaly, long narrow face, high forehead, slender habitus, scoliosis, and unusual behavior characterized especially by anxiety. {ECO:0000269|PubMed:20673863, ECO:0000269|PubMed:22301465, ECO:0000269|PubMed:26193383, ECO:0000269|PubMed:26200704}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Marshall-Smith syndrome (MRSHSS) [MIM:602535]: A distinct malformation syndrome characterized by accelerated skeletal maturation, relative failure to thrive, respiratory difficulties, mental retardation, and unusual facies, including prominent forehead, shallow orbits, blue sclerae, depressed nasal bridge, and micrognathia. Additional skeletal findings include long and thin tubular bones, broad middle phalanges with relatively narrow distal phalanges, and scoliosis. {ECO:0000269|PubMed:20673863, ECO:0000269|PubMed:26200704}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Recognizes and binds the palindromic sequence 5'- TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.; ",{"$nulls":4},"p.Ser322Phe","c.965C>T","MODERATE","322/502",7,{"$nulls":5},"4","442","537","313","372","377","436","0","0","0","0.2294",{"$nulls":20},"4.099316","0.92","2.43;2.43;.;.;.;.","1","-2.3;.;.;.;.;.","0.925;0.979;.;.;.;0.925","0.004;.;.;.;.;.","0.625;0.545;0.54;0.627;0.459;0.557",{"$nulls":3},"Unknown",-1,"AD","Marshall-Smithsyndrome; Sotos syndrome 2","Craniofacial; Musculoskeletal; Neurologic; Pulmonary",{"$nulls":3},"C0265211| C3553660","0/0","416,0","0","416","0/1","376,110","0.2263","486",null,"chr19:13078622:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2339"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","NFIX","chr19:13078622","NFIX(S322F)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense",null,-1,"DISEASE: Sotos syndrome 2 (SOTOS2) [MIM:614753]: A form of Sotos syndrome, a childhood overgrowth syndrome characterized by prenatal and postnatal overgrowth, developmental delay, mental retardation, advanced bone age, and abnormal craniofacial morphology. SOTOS2 patients have macrocephaly, long narrow face, high forehead, slender habitus, scoliosis, and unusual behavior characterized especially by anxiety. {ECO:0000269|PubMed:20673863, ECO:0000269|PubMed:22301465, ECO:0000269|PubMed:26193383, ECO:0000269|PubMed:26200704}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Marshall-Smith syndrome (MRSHSS) [MIM:602535]: A distinct malformation syndrome characterized by accelerated skeletal maturation, relative failure to thrive, respiratory difficulties, mental retardation, and unusual facies, including prominent forehead, shallow orbits, blue sclerae, depressed nasal bridge, and micrognathia. Additional skeletal findings include long and thin tubular bones, broad middle phalanges with relatively narrow distal phalanges, and scoliosis. {ECO:0000269|PubMed:20673863, ECO:0000269|PubMed:26200704}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Recognizes and binds the palindromic sequence 5'- TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.; ",{"$nulls":4},"p.Ser322Phe","c.965C>T","MODERATE","322/502",7,{"$nulls":5},"4","442","500","313","357","376","400","0","0","0","0.1275",{"$nulls":20},"4.099316","0.92","2.43;2.43;.;.;.;.","1","-2.3;.;.;.;.;.","0.925;0.979;.;.;.;0.925","0.004;.;.;.;.;.","0.625;0.545;0.54;0.627;0.459;0.557",{"$nulls":3},"Unknown",-1,"AD","Marshall-Smithsyndrome; Sotos syndrome 2","Craniofacial; Musculoskeletal; Neurologic; Pulmonary",{"$nulls":3},"C0265211| C3553660","0/0","415,0","0","415","0/1","395,64","0.1394","459",null,"chr19:13078622:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1373"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","NHLRC2","chr10:113904989","NHLRC2(S626*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ser626*","c.1877C>G","HIGH","626/726",10,{"$nulls":5},"5","293","258","194","168","273","237","0","0","0","0.3291",{"$nulls":20},"6.397502",null,null,"1",{"$nulls":3},"0.025",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748939","0/0","285,0","0","285","0/1","166,88","0.3465","254",null,"chr10:113904989:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3333"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","NHLRC2","chr10:113904989","NHLRC2(S626*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Ser626*","c.1877C>G","HIGH","626/726",10,{"$nulls":5},"5","293","300","194","189","270","271","0","0","0","0.3395",{"$nulls":20},"6.397502",null,null,"1",{"$nulls":3},"0.025",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4748939","0/0","285,0","0","285","0/1","180,103","0.364","283",null,"chr10:113904989:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3651"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","NPAS4","chr11:66425043","NPAS4(S718C)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor expressed in neurons of the brain that regulates the excitatory-inhibitory balance within neural circuits and is required for contextual memory in the hyppocampus (By similarity). Plays a key role in the structural and functional plasticity of neurons (By similarity). Acts as an early-response transcription factor in both excitatory and inhibitory neurons, where it induces distinct but overlapping sets of late-response genes in these two types of neurons, allowing the synapses that form on inhibitory and excitatory neurons to be modified by neuronal activity in a manner specific to their function within a circuit, thereby facilitating appropriate circuit responses to sensory experience (By similarity). In excitatory neurons, activates transcription of BDNF, which in turn controls the number of GABA-releasing synapses that form on excitatory neurons, thereby promoting an increased number of inhibitory synapses on excitatory neurons (By similarity). In inhibitory neurons, regulates a distinct set of target genes that serve to increase excitatory input onto somatostatin neurons, probably resulting in enhanced feedback inhibition within cortical circuits (By similarity). The excitatory and inhibitory balance in neurons affects a number of processes, such as short-term and long-term memory, acquisition of experience, fear memory, response to stress and social behavior (By similarity). Acts as a regulator of dendritic spine development in olfactory bulb granule cells in a sensory-experience-dependent manner by regulating expression of MDM2 (By similarity). Efficient DNA binding requires dimerization with another bHLH protein, such as ARNT, ARNT2 or BMAL1 (PubMed:14701734). Can activate the CME (CNS midline enhancer) element (PubMed:14701734). {ECO:0000250|UniProtKB:Q8BGD7, ECO:0000269|PubMed:14701734}.; ",{"$nulls":4},"p.Ser718Cys","c.2153C>G","MODERATE","718/802",7,{"$nulls":5},"5","547","543","411","394","497","467","0","0","0","0.3704",{"$nulls":20},"3.505329","0.75","1.525","0.993868","-1.01","0.997","0.002","0.531",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","522,0","0","522","0/1","322,194","0.376","516",null,"chr11:66425043:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3553"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","NPAS4","chr11:66425043","NPAS4(S718C)",null,null,"splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Transcription factor expressed in neurons of the brain that regulates the excitatory-inhibitory balance within neural circuits and is required for contextual memory in the hyppocampus (By similarity). Plays a key role in the structural and functional plasticity of neurons (By similarity). Acts as an early-response transcription factor in both excitatory and inhibitory neurons, where it induces distinct but overlapping sets of late-response genes in these two types of neurons, allowing the synapses that form on inhibitory and excitatory neurons to be modified by neuronal activity in a manner specific to their function within a circuit, thereby facilitating appropriate circuit responses to sensory experience (By similarity). In excitatory neurons, activates transcription of BDNF, which in turn controls the number of GABA-releasing synapses that form on excitatory neurons, thereby promoting an increased number of inhibitory synapses on excitatory neurons (By similarity). In inhibitory neurons, regulates a distinct set of target genes that serve to increase excitatory input onto somatostatin neurons, probably resulting in enhanced feedback inhibition within cortical circuits (By similarity). The excitatory and inhibitory balance in neurons affects a number of processes, such as short-term and long-term memory, acquisition of experience, fear memory, response to stress and social behavior (By similarity). Acts as a regulator of dendritic spine development in olfactory bulb granule cells in a sensory-experience-dependent manner by regulating expression of MDM2 (By similarity). Efficient DNA binding requires dimerization with another bHLH protein, such as ARNT, ARNT2 or BMAL1 (PubMed:14701734). Can activate the CME (CNS midline enhancer) element (PubMed:14701734). {ECO:0000250|UniProtKB:Q8BGD7, ECO:0000269|PubMed:14701734}.; ",{"$nulls":4},"p.Ser718Cys","c.2153C>G","MODERATE","718/802",7,{"$nulls":5},"5","547","637","411","474","495","559","0","0","0","0.2826",{"$nulls":20},"3.505329","0.75","1.525","0.993868","-1.01","0.997","0.002","0.531",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","519,0","0","519","0/1","399,170","0.2988","569",null,"chr11:66425043:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2764"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","NT5C3A","chr7:33062613","NT5C3A(F36L)",null,null,"splice variant (In isoform 4. ), splice variant (In isoform 1. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: P5N deficiency (P5ND) [MIM:266120]: Autosomal recessive condition causing hemolytic anemia characterized by marked basophilic stippling and the accumulation of high concentrations of pyrimidine nucleotides within the erythrocyte. It is implicated in the anemia of lead poisoning and is possibly associated with learning difficulties. {ECO:0000269|PubMed:11369620, ECO:0000269|PubMed:12930399, ECO:0000269|PubMed:15238149, ECO:0000269|PubMed:15604219, ECO:0000269|PubMed:15968458, ECO:0000269|PubMed:16461318, ECO:0000269|PubMed:18499901, ECO:0000269|PubMed:25153905}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Nucleotidase which shows specific activity towards cytidine monophosphate (CMP) and 7-methylguanosine monophosphate (m(7)GMP) (PubMed:24603684). CMP seems to be the preferred substrate (PubMed:15968458). {ECO:0000269|PubMed:15968458, ECO:0000269|PubMed:24603684}.; ",{"$nulls":4},"p.Phe36Leu","c.108C>A","MODERATE","36/336",1,1,{"$nulls":4},"5","372","347","295","271","332","178","0","0","0","0.3146",{"$nulls":20},"2.627793",null,".;0.55;.","0.989387",null,".;0.002;.",null,".;0.32;0.324",{"$nulls":3},"Unknown",-1,"AR","Uridine 5-prime monophosphate hydrolase deficiency, hemolytic anemia due to","Hematologic",{"$nulls":3},"C1849507","0/0","362,0","0","362","0/1","213,127","0.3735","340",null,"chr7:33062613:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3838"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","NT5C3A","chr7:33062613","NT5C3A(F36L)",null,null,"splice variant (In isoform 4. ), splice variant (In isoform 1. ), splice variant (In isoform 3. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: P5N deficiency (P5ND) [MIM:266120]: Autosomal recessive condition causing hemolytic anemia characterized by marked basophilic stippling and the accumulation of high concentrations of pyrimidine nucleotides within the erythrocyte. It is implicated in the anemia of lead poisoning and is possibly associated with learning difficulties. {ECO:0000269|PubMed:11369620, ECO:0000269|PubMed:12930399, ECO:0000269|PubMed:15238149, ECO:0000269|PubMed:15604219, ECO:0000269|PubMed:15968458, ECO:0000269|PubMed:16461318, ECO:0000269|PubMed:18499901, ECO:0000269|PubMed:25153905}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Nucleotidase which shows specific activity towards cytidine monophosphate (CMP) and 7-methylguanosine monophosphate (m(7)GMP) (PubMed:24603684). CMP seems to be the preferred substrate (PubMed:15968458). {ECO:0000269|PubMed:15968458, ECO:0000269|PubMed:24603684}.; ",{"$nulls":4},"p.Phe36Leu","c.108C>A","MODERATE","36/336",1,1,{"$nulls":4},"5","372","399","295","310","330","189","0","0","0","0.1534",{"$nulls":20},"2.627793",null,".;0.55;.","0.989387",null,".;0.002;.",null,".;0.32;0.324",{"$nulls":3},"Unknown",-1,"AR","Uridine 5-prime monophosphate hydrolase deficiency, hemolytic anemia due to","Hematologic",{"$nulls":3},"C1849507","0/0","366,0","0","366","0/1","322,71","0.1807","393",null,"chr7:33062613:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1742"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","OR10K2","chr1:158420782","OR10K2(V29F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Val29Phe","c.85G>T","MODERATE","29/312",1,{"$nulls":5},"5","340","253","254","181","307","166","0","0","0","0.3253",{"$nulls":20},"-0.967646",".;7.25","0.945","1",".;-2.44","0.002",".;0.198",".;0.198",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","328,0","0","328","0/1","156,85","0.3527","241",null,"chr1:158420782:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3425"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","OR10K2","chr1:158420782","OR10K2(V29F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Val29Phe","c.85G>T","MODERATE","29/312",1,{"$nulls":5},"5","340","333","254","232","309","197","0","0","0","0.4315",{"$nulls":20},"-0.967646",".;7.25","0.945","1",".;-2.44","0.002",".;0.198",".;0.198",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","335,0","0","335","0/1","183,140","0.4334","323",null,"chr1:158420782:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4353"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","OR2Y1","chr5:180739800","OR2Y1(G87R)",{"$nulls":6},255,"PASS","Missense","rs369440057",2.3255813953488373E-4,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Gly87Arg","c.259G>A","MODERATE","87/311",1,{"$nulls":5},"5","229","278","187","211","215","247","0.0044","0.0044","0","0.251",{"$nulls":20},"0.87804","4.37","1.64","1","-5.44","0.358","0.043","0.146",{"$nulls":3},"ESP6500_EA_AF",2.3255813953488373E-4,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","225,1","0.0044","226","0/1","202,71","0.2601","273",null,"chr5:180739800:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2749"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","OR2Y1","chr5:180739800","OR2Y1(G87R)",{"$nulls":6},255,"PASS","Missense","rs369440057",2.3255813953488373E-4,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Gly87Arg","c.259G>A","MODERATE","87/311",1,{"$nulls":5},"4","229","317","187","248",null,null,"0.0044","0.0044",{"$nulls":22},"0.87804","4.37","1.64","1","-5.44","0.358","0.043","0.146",{"$nulls":3},"ESP6500_EA_AF",2.3255813953488373E-4,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].",null,null,"0/0","225,1","0.0044","226","0/1","233,78","0.2508","311",null,"chr5:180739800:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2702"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","OR4C13","chr11:49952577","OR4C13(S52L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser52Leu","c.155C>T","MODERATE","52/309",1,{"$nulls":5},"5","633","653","430","437","572","584","0","0","0","0.3339",{"$nulls":20},"-0.933211","5.35","1.865","1","-0.57",null,"0.42","0.073",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","584,0","0","584","0/1","400,210","0.3443","610",null,"chr11:49952577:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3341"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","OR4C13","chr11:49952577","OR4C13(S52L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Odorant receptor. {ECO:0000305}.; ",{"$nulls":4},"p.Ser52Leu","c.155C>T","MODERATE","52/309",1,{"$nulls":5},"5","633","765","430","520","572","684","0","0","0","0.2661",{"$nulls":20},"-0.933211","5.35","1.865","1","-0.57",null,"0.42","0.073",{"$nulls":3},"Unknown",-1,{"$nulls":4},"Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008].  ",null,null,"0/0","585,0","0","585","0/1","523,180","0.256","703",null,"chr11:49952577:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2635"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ORAOV1","chr11:69673301","ORAOV1(R24Q)",{"$nulls":6},255,"PASS","Missense","rs754688184",8.639e-05,{"$nulls":6},"p.Arg24Gln","c.71G>A","MODERATE","24/221",2,{"$nulls":5},"5","499","565","335","377","459","502","0","0","0","0.1155",{"$nulls":20},"0.746481","0.76",null,"1;0.988876;0.988876;0.988876;0.988876","0.87;1.14;1.14;0.93;0.97","0.241;0.0;0.0;.;0.0","1.0","0.238;0.255;0.25;0.263;0.247",{"$nulls":3},"ExAC_AMR_AF",8.639e-05,{"$nulls":7},"0/0","473,0","0","473","0/1","472,73","0.1339","545",null,"chr11:69673301:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.13"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","OTOA","chr16:21715063","OTOA(R481C)",{"$nulls":6},255,"PASS","Missense","rs757720270",1.499E-5,"DISEASE: Deafness, autosomal recessive, 22 (DFNB22) [MIM:607039]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:11972037}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: May act as an adhesion molecule.; ",{"$nulls":4},"p.Arg481Cys","c.1441C>T","MODERATE","481/1153",13,2,{"$nulls":4},"5","407","779","305","566","333","650","0","0","0","0.1015",{"$nulls":20},"1.201881",".;-1.18;-1.18;-1.18;-1.18",".;0.83;.;.;.","1",".;-1.86;-1.88;-1.88;-1.82",".;0.992;.;.;0.996",".;0.103;0.1;0.086;0.116",".;0.166;0.158;0.188;0.167",{"$nulls":3},"ExAC_NFE_AF",1.499E-5,"AR","Deafness, autosomal recessive 22","Audiologic/Otolaryngologic",null,"The protein encoded by this gene is specifically expressed in the inner ear, and is located at the interface between the apical surface of the inner ear sensory epithelia and their overlying acellular gels. It is prposed that this protein is involved in the attachment of the inner ear acellular gels to the apical surface of the underlying nonsensory cells. Mutations in this gene are associated with autosomal recessive deafness type 22 (DFNB22). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009].",null,"C1846896","0/0","388,0","0","388","0/1","673,74","0.0991","747",null,"chr16:21715063:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0954"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","OTOR","chr20:16749919","OTOR(Q91P)",null,null,"domain (SH3 ), disulfide bond ",{"$nulls":3},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Gln91Pro","c.272A>C","MODERATE","91/128",3,{"$nulls":5},"5","584","337","404","232","503","284","0","0","0","0.088",{"$nulls":20},"2.073768","-1.5","1.1","0.596294","-1.51","0.09","0.208","0.603",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","537,0","0","537","0/1","277,29","0.0948","306",null,"chr20:16749919:A:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0948"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","OTUD7A","chr15:31483317","OTUD7A(E920K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Has deubiquitinating activity towards 'Lys-11'-linked polyubiquitin chains. {ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:23827681}.; ","gedi",{"$nulls":3},"p.Glu920Lys","c.2758G>A","MODERATE","920/926",11,{"$nulls":5},"5","179","67","146","55","127","55","0","0","0","0.6",{"$nulls":20},"2.622833","1.55","0.75","0.572342","-0.46","0.458","0.085","0.085",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","173,0","0","173","0/1","30,35","0.5385","65",null,"chr15:31483317:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5273"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","OTUD7A","chr15:31483317","OTUD7A(E920K)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Has deubiquitinating activity towards 'Lys-11'-linked polyubiquitin chains. {ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:23827681}.; ","gedi",{"$nulls":3},"p.Glu920Lys","c.2758G>A","MODERATE","920/926",11,{"$nulls":5},"5","179","128","146","110","128","107","0","0","0","0.4766",{"$nulls":20},"2.622833","1.55","0.75","0.572342","-0.46","0.458","0.085","0.085",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","174,0","0","174","0/1","72,51","0.4146","123",null,"chr15:31483317:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4091"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","P2RX5-TAX1BP3","chr17:3691760","P2RX5-TAX1BP3(V58I)",{"$nulls":6},255,"PASS","Missense","rs534631748",1.440922190201729E-3,{"$nulls":6},"p.Val58Ile","c.172G>A","MODERATE","58/432",2,{"$nulls":5},"5","1103","1020","760","673","1016","927","0","0","0","0.0626",{"$nulls":20},"0.784602","3.66",".;0.55;0.55;0.55;0.55;.","1",".;-0.47;-0.49;-0.49;-0.47;-0.44",".;0.037;0.037;0.046;.;0.14",".;0.72;0.313;0.311;0.376;0.351","0.111;0.152;0.112;0.113;0.155;0.087",{"$nulls":3},"1000Gp3_AMR_AF",1.440922190201729E-3,{"$nulls":7},"0/0","1038,1","0.001","1039","0/1","879,67","0.0708","946",null,"chr17:3691760:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0594"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","PDE6D","chr2:231737266","PDE6D(I98F)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Promotes the release of prenylated target proteins from cellular membranes (PubMed:9712853). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22002721, PubMed:23698361). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (PubMed:24166846). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (By similarity). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate (By similarity). {ECO:0000250|UniProtKB:O55057, ECO:0000269|PubMed:10518933, ECO:0000269|PubMed:22002721, ECO:0000269|PubMed:23559067, ECO:0000269|PubMed:23698361, ECO:0000269|PubMed:24166846, ECO:0000269|PubMed:9712853}.; ",{"$nulls":4},"p.Ile98Phe","c.292A>T","MODERATE","98/150",4,{"$nulls":5},"4","458","360","282","230","428","331","0","0","0","0.0695",{"$nulls":20},"4.343604",null,"2.945;.","1","-2.85;-2.92","0.79;.","0.022;0.005","0.879;.",{"$nulls":3},"Unknown",-1,"AR","Joubert syndrome 22","Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic; Renal",{"$nulls":3},"C3810278","0/0","447,0","0","447","0/1","324,26","0.0743","350",null,"chr2:231737266:T:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0783"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","PGS1","chr17:78400756","PGS1(F261fs)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin. {ECO:0000250}.; ","mitocarta",{"$nulls":3},"p.Phe261fs","c.781_792del<DELETE_NUC>insT","HIGH","261/556",6,{"$nulls":20},"78401628",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr17:78400756:<DELETE_NUC>:T",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","PHKA1","chrX:72582534","PHKA1(P1138R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glycogen storage disease 9D (GSD9D) [MIM:300559]: A metabolic disorder characterized by slowly progressive, predominantly distal muscle weakness and atrophy. Clinical features include exercise intolerance with early fatigability, pain, cramps and occasionally myoglobinuria. {ECO:0000269|PubMed:12825073}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Phosphorylase b kinase catalyzes the phosphorylation of serine in certain substrates, including troponin I. The alpha chain may bind calmodulin.; ",{"$nulls":4},"p.Pro1138Arg","c.3413C>G","MODERATE","1138/1240",32,{"$nulls":5},"5","376","319","246","206","352","282","0","0","0","0.3617",{"$nulls":20},"3.832623","-4.0;-4.09;-3.95;-4.03;-4.13","3.53;.;.;.;.","1","-8.49;-8.44;-8.49;-8.59;-8.49","1.0;1.0;1.0;.;.","0.0","0.954;0.948;0.899;0.954;0.953",{"$nulls":3},"Unknown",-1,"XL","Glycogen storage disease, type Ixd","Biochemical; Musculoskeletal; Renal",{"$nulls":3},"C1845151","0/0","368,0","0","368","0/1","193,112","0.3672","305",null,"chrX:72582534:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3544"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","PHKA1","chrX:72582534","PHKA1(P1138R)",{"$nulls":6},255,"PASS","Missense",null,-1,"DISEASE: Glycogen storage disease 9D (GSD9D) [MIM:300559]: A metabolic disorder characterized by slowly progressive, predominantly distal muscle weakness and atrophy. Clinical features include exercise intolerance with early fatigability, pain, cramps and occasionally myoglobinuria. {ECO:0000269|PubMed:12825073}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Phosphorylase b kinase catalyzes the phosphorylation of serine in certain substrates, including troponin I. The alpha chain may bind calmodulin.; ",{"$nulls":4},"p.Pro1138Arg","c.3413C>G","MODERATE","1138/1240",32,{"$nulls":5},"5","376","361","246","250","351","325","0","0","0","0.2462",{"$nulls":20},"3.832623","-4.0;-4.09;-3.95;-4.03;-4.13","3.53;.;.;.;.","1","-8.49;-8.44;-8.49;-8.59;-8.49","1.0;1.0;1.0;.;.","0.0","0.954;0.948;0.899;0.954;0.953",{"$nulls":3},"Unknown",-1,"XL","Glycogen storage disease, type Ixd","Biochemical; Musculoskeletal; Renal",{"$nulls":3},"C1845151","0/0","369,0","0","369","0/1","266,93","0.2591","359",null,"chrX:72582534:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.264"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","PLIN4","chr19:4516643","PLIN4(E78Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in triacylglycerol packaging into adipocytes. May function as a coat protein involved in the biogenesis of lipid droplets (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu78Gln","c.232G>C","MODERATE","78/1372",4,{"$nulls":5},"5","280","389","198","263","210","273","0","0","0","0.2527",{"$nulls":20},"0.6084","3.78;.","1.5;.","1","-0.88;.","0.596;.","0.478;.","0.347;0.325",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","265,0","0","265","0/1","252,103","0.2901","355",null,"chr19:4516643:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3156"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","PLIN4","chr19:4516643","PLIN4(E78Q)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: May play a role in triacylglycerol packaging into adipocytes. May function as a coat protein involved in the biogenesis of lipid droplets (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Glu78Gln","c.232G>C","MODERATE","78/1372",4,{"$nulls":5},"5","280","352","198","230","209","268","0","0","0","0.1343",{"$nulls":20},"0.6084","3.78;.","1.5;.","1","-0.88;.","0.596;.","0.478;.","0.347;0.325",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","264,0","0","264","0/1","289,47","0.1399","336",null,"chr19:4516643:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1522"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","POGZ","chr1:151404858","POGZ(E1393*)",null,null,"short sequence motif (Integrase domain-binding motif (IBM) ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Defects in POGZ may be associated with neuropsychiatric disorders such as autism spectrum disorders (ASD), bipolar affective disorders and early dementia onset. ASD are characterized by impairments in reciprocal social interaction and communication as well as restricted and stereotyped patterns of interest and activities. ASD include forms with moderate to severe cognitive impairment and milder forms with higher cognitive ability (Asperger syndrome). {ECO:0000269|PubMed:25694107}.; DISEASE: White-Sutton syndrome (WHSUS) [MIM:616364]: A mental retardation syndrome characterized by developmental delay, intellectual disability, hypotonia, behavioral abnormalities, and dysmorphic facial features. Variable features include short stature, microcephaly, strabismus and hearing loss. {ECO:0000269|PubMed:25533962, ECO:0000269|PubMed:26739615}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in mitotic cell cycle progression and is involved in kinetochore assembly and mitotic sister chromatid cohesion. Probably through its association with CBX5 plays a role in mitotic chromosome segregation by regulating aurora kinase B/AURKB activation and AURKB and CBX5 dissociation from chromosome arms. {ECO:0000269|PubMed:20562864}.; ",{"$nulls":4},"p.Glu1393*","c.4177G>T","HIGH","1393/1410",19,{"$nulls":5},"4","283","323","231","268","228","244","0.0035","0.0035","0","0.4139",{"$nulls":20},"7.624169",null,null,"1",{"$nulls":3},"0.334;0.379;0.325;0.42;0.34;0.351",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225351","0/0","278,1","0.0036","279","0/1","196,121","0.3817","317",null,"chr1:151404858:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3806"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","POGZ","chr1:151404858","POGZ(E1393*)",null,null,"short sequence motif (Integrase domain-binding motif (IBM) ), splice variant (In isoform 4. )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,"DISEASE: Note=Defects in POGZ may be associated with neuropsychiatric disorders such as autism spectrum disorders (ASD), bipolar affective disorders and early dementia onset. ASD are characterized by impairments in reciprocal social interaction and communication as well as restricted and stereotyped patterns of interest and activities. ASD include forms with moderate to severe cognitive impairment and milder forms with higher cognitive ability (Asperger syndrome). {ECO:0000269|PubMed:25694107}.; DISEASE: White-Sutton syndrome (WHSUS) [MIM:616364]: A mental retardation syndrome characterized by developmental delay, intellectual disability, hypotonia, behavioral abnormalities, and dysmorphic facial features. Variable features include short stature, microcephaly, strabismus and hearing loss. {ECO:0000269|PubMed:25533962, ECO:0000269|PubMed:26739615}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Plays a role in mitotic cell cycle progression and is involved in kinetochore assembly and mitotic sister chromatid cohesion. Probably through its association with CBX5 plays a role in mitotic chromosome segregation by regulating aurora kinase B/AURKB activation and AURKB and CBX5 dissociation from chromosome arms. {ECO:0000269|PubMed:20562864}.; ",{"$nulls":4},"p.Glu1393*","c.4177G>T","HIGH","1393/1410",19,{"$nulls":5},"4","283","465","231","374","229","397","0.0035","0.0035","0","0.4433",{"$nulls":20},"7.624169",null,null,"1",{"$nulls":3},"0.334;0.379;0.325;0.42;0.34;0.351",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4225351","0/0","277,1","0.0036","278","0/1","261,182","0.4108","443",null,"chr1:151404858:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4091"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","PRKCI","chr3:170270438","PRKCI(I156M)",null,null,"zinc finger region (Phorbol-ester/DAG-type ), region of interest (Regulatory domain )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium- and diacylglycerol-independent serine/ threonine-protein kinase that plays a general protective role against apoptotic stimuli, is involved in NF-kappa-B activation, cell survival, differentiation and polarity, and contributes to the regulation of microtubule dynamics in the early secretory pathway. Is necessary for BCR-ABL oncogene-mediated resistance to apoptotic drug in leukemia cells, protecting leukemia cells against drug-induced apoptosis. In cultured neurons, prevents amyloid beta protein-induced apoptosis by interrupting cell death process at a very early step. In glioblastoma cells, may function downstream of phosphatidylinositol 3-kinase (PI(3)K) and PDPK1 in the promotion of cell survival by phosphorylating and inhibiting the pro-apoptotic factor BAD. Can form a protein complex in non- small cell lung cancer (NSCLC) cells with PARD6A and ECT2 and regulate ECT2 oncogenic activity by phosphorylation, which in turn promotes transformed growth and invasion. In response to nerve growth factor (NGF), acts downstream of SRC to phosphorylate and activate IRAK1, allowing the subsequent activation of NF-kappa-B and neuronal cell survival. Functions in the organization of the apical domain in epithelial cells by phosphorylating EZR. This step is crucial for activation and normal distribution of EZR at the early stages of intestinal epithelial cell differentiation. Forms a protein complex with LLGL1 and PARD6B independently of PARD3 to regulate epithelial cell polarity. Plays a role in microtubule dynamics in the early secretory pathway through interaction with RAB2A and GAPDH and recruitment to vesicular tubular clusters (VTCs). In human coronary artery endothelial cells (HCAEC), is activated by saturated fatty acids and mediates lipid-induced apoptosis. {ECO:0000269|PubMed:10356400, ECO:0000269|PubMed:10467349, ECO:0000269|PubMed:10906326, ECO:0000269|PubMed:11042363, ECO:0000269|PubMed:11724794, ECO:0000269|PubMed:12871960, ECO:0000269|PubMed:14684752, ECO:0000269|PubMed:15994303, ECO:0000269|PubMed:18270268, ECO:0000269|PubMed:19327373, ECO:0000269|PubMed:21189248, ECO:0000269|PubMed:21419810, ECO:0000269|PubMed:8226978, ECO:0000269|PubMed:9346882}.; ",null,"[ \"Auranofin\"]","[ \"Auranofin\"]","[ \"Auranofin\"]","p.Ile156Met","c.468C>G","MODERATE","156/596",6,1,{"$nulls":4},"5","403","462","302","368","290","363","0","0","0","0.6143",{"$nulls":20},"3.169495","-3.12","1.385","1","0.09","0.952","0.184","0.752",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","371,0","0","371","0/1","191,239","0.5558","430",null,"chr3:170270438:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5598"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","PRKCI","chr3:170270438","PRKCI(I156M)",null,null,"zinc finger region (Phorbol-ester/DAG-type ), region of interest (Regulatory domain )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Calcium- and diacylglycerol-independent serine/ threonine-protein kinase that plays a general protective role against apoptotic stimuli, is involved in NF-kappa-B activation, cell survival, differentiation and polarity, and contributes to the regulation of microtubule dynamics in the early secretory pathway. Is necessary for BCR-ABL oncogene-mediated resistance to apoptotic drug in leukemia cells, protecting leukemia cells against drug-induced apoptosis. In cultured neurons, prevents amyloid beta protein-induced apoptosis by interrupting cell death process at a very early step. In glioblastoma cells, may function downstream of phosphatidylinositol 3-kinase (PI(3)K) and PDPK1 in the promotion of cell survival by phosphorylating and inhibiting the pro-apoptotic factor BAD. Can form a protein complex in non- small cell lung cancer (NSCLC) cells with PARD6A and ECT2 and regulate ECT2 oncogenic activity by phosphorylation, which in turn promotes transformed growth and invasion. In response to nerve growth factor (NGF), acts downstream of SRC to phosphorylate and activate IRAK1, allowing the subsequent activation of NF-kappa-B and neuronal cell survival. Functions in the organization of the apical domain in epithelial cells by phosphorylating EZR. This step is crucial for activation and normal distribution of EZR at the early stages of intestinal epithelial cell differentiation. Forms a protein complex with LLGL1 and PARD6B independently of PARD3 to regulate epithelial cell polarity. Plays a role in microtubule dynamics in the early secretory pathway through interaction with RAB2A and GAPDH and recruitment to vesicular tubular clusters (VTCs). In human coronary artery endothelial cells (HCAEC), is activated by saturated fatty acids and mediates lipid-induced apoptosis. {ECO:0000269|PubMed:10356400, ECO:0000269|PubMed:10467349, ECO:0000269|PubMed:10906326, ECO:0000269|PubMed:11042363, ECO:0000269|PubMed:11724794, ECO:0000269|PubMed:12871960, ECO:0000269|PubMed:14684752, ECO:0000269|PubMed:15994303, ECO:0000269|PubMed:18270268, ECO:0000269|PubMed:19327373, ECO:0000269|PubMed:21189248, ECO:0000269|PubMed:21419810, ECO:0000269|PubMed:8226978, ECO:0000269|PubMed:9346882}.; ",null,"[ \"Auranofin\"]","[ \"Auranofin\"]","[ \"Auranofin\"]","p.Ile156Met","c.468C>G","MODERATE","156/596",6,1,{"$nulls":4},"5","403","532","302","417","292","394","0","0","0","0.3604",{"$nulls":20},"3.169495","-3.12","1.385","1","0.09","0.952","0.184","0.752",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","373,0","0","373","0/1","316,187","0.3718","503",null,"chr3:170270438:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3765"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","RASAL2","chr1:178390166","RASAL2(N175S)",null,null,"domain (C2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibitory regulator of the Ras-cyclic AMP pathway.; ",{"$nulls":4},"p.Asn175Ser","c.524A>G","MODERATE","175/1280",4,{"$nulls":5},"5","218","231","153","144","203","196","0","0","0","0.3469",{"$nulls":20},"0.937649","2.23;2.24",".;1.04","0.942426;0.907896;0.942426","-0.47;-0.33",".;0.495","0.437;0.48","0.283;0.253",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","210,0","0","210","0/1","137,81","0.3716","218",null,"chr1:178390166:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3819"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","RASAL2","chr1:178390166","RASAL2(N175S)",null,null,"domain (C2 )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Inhibitory regulator of the Ras-cyclic AMP pathway.; ",{"$nulls":4},"p.Asn175Ser","c.524A>G","MODERATE","175/1280",4,{"$nulls":5},"5","218","229","153","148","202","199","0","0","0","0.1357",{"$nulls":20},"0.937649","2.23;2.24",".;1.04","0.942426;0.907896;0.942426","-0.47;-0.33",".;0.495","0.437;0.48","0.283;0.253",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","212,0","0","212","0/1","191,30","0.1357","221",null,"chr1:178390166:A:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1486"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","RASAL3","chr19:15453285","RASAL3(S831F)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense","rs1321563744",-1,null,"FUNCTION: Functions as a Ras GTPase-activating protein. Plays an important role in the expansion and functions of natural killer T (NKT) cells in the liver by negatively regulating RAS activity and the down-stream ERK signaling pathway. {ECO:0000250|UniProtKB:Q8C2K5}.; ",{"$nulls":4},"p.Ser831Phe","c.2492C>T","MODERATE","831/1011",15,{"$nulls":5},"5","210","324","179","282","180","262","0","0","0","0.229",{"$nulls":20},"2.442182",".;1.73",".;2.075","1",".;-2.31",".;0.838",".;0.0",".;0.332",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","207,0","0","207","0/1","240,78","0.2453","318",null,"chr19:15453285:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2411"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","RASAL3","chr19:15453285","RASAL3(S831F)",{"$nulls":3},"modified-residue:phosphoserine","MODERATE",null,255,"PASS","Missense","rs1321563744",-1,null,"FUNCTION: Functions as a Ras GTPase-activating protein. Plays an important role in the expansion and functions of natural killer T (NKT) cells in the liver by negatively regulating RAS activity and the down-stream ERK signaling pathway. {ECO:0000250|UniProtKB:Q8C2K5}.; ",{"$nulls":4},"p.Ser831Phe","c.2492C>T","MODERATE","831/1011",15,{"$nulls":5},"5","210","285","179","244","180","243","0","0","0","0.1317",{"$nulls":20},"2.442182",".;1.73",".;2.075","1",".;-2.31",".;0.838",".;0.0",".;0.332",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","207,0","0","207","0/1","247,38","0.1333","285",null,"chr19:15453285:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.123"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","RBMXL3","chrX:115189811","RBMXL3(Q124*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gln124*","c.370C>T","HIGH","124/1067",1,{"$nulls":5},"4","902","761","674","580","801","668","0","0","0","0.3293",{"$nulls":20},"3.76776",null,null,"1",{"$nulls":3},"0.057",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","874,0","0","874","0/1","499,232","0.3174","731",null,"chrX:115189811:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3172"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","RBMXL3","chrX:115189811","RBMXL3(Q124*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Gln124*","c.370C>T","HIGH","124/1067",1,{"$nulls":5},"4","902","1142","674","867","799","994","0","0","0","0.3712",{"$nulls":20},"3.76776",null,null,"1",{"$nulls":3},"0.057",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","872,0","0","872","0/1","685,423","0.3818","1108",null,"chrX:115189811:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3852"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","REXO1","chr19:1848211","REXO1(P50S)",{"$nulls":6},255,"PASS","Missense","rs1035427492",-1,null,"FUNCTION: Seems to have no detectable effect on transcription elongation in vitro. {ECO:0000269|PubMed:12943681}.; ",{"$nulls":4},"p.Pro50Ser","c.148C>T","MODERATE","50/1221",1,{"$nulls":5},"5","39","21","32","19","31","16","0","0","0","0.625",{"$nulls":20},"1.497044","2.81","2.25","1","-0.8","0.075","0.311","0.081",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","39,0","0","39","0/1","8,12","0.6","20",null,"chr19:1848211:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5789"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","REXO1","chr19:1848211","REXO1(P50S)",{"$nulls":6},255,"PASS","Missense","rs1035427492",-1,null,"FUNCTION: Seems to have no detectable effect on transcription elongation in vitro. {ECO:0000269|PubMed:12943681}.; ",{"$nulls":4},"p.Pro50Ser","c.148C>T","MODERATE","50/1221",1,{"$nulls":5},"5","39","35","32","29","31","25","0","0","0","0.64",{"$nulls":20},"1.497044","2.81","2.25","1","-0.8","0.075","0.311","0.081",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","39,0","0","39","0/1","12,21","0.6364","33",null,"chr19:1848211:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6207"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","RLIM","chrX:74592201","RLIM(R372G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex- related dosage differences of X-encoded genes in somatic cells of female placental mammals. {ECO:0000269|PubMed:19164295, ECO:0000269|PubMed:19945382}.; ",{"$nulls":4},"p.Arg372Gly","c.1114C>G","MODERATE","372/624",4,{"$nulls":5},"5","611","448","479","332","521","387","0","0","0","0.3488",{"$nulls":20},"3.509258","2.54","2.67","1","-5.38","1.0","0.002","0.726;0.737",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4283894","0/0","582,0","0","582","0/1","275,136","0.3309","411",null,"chrX:74592201:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3283"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","RLIM","chrX:74592201","RLIM(R372G)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex- related dosage differences of X-encoded genes in somatic cells of female placental mammals. {ECO:0000269|PubMed:19164295, ECO:0000269|PubMed:19945382}.; ",{"$nulls":4},"p.Arg372Gly","c.1114C>G","MODERATE","372/624",4,{"$nulls":5},"5","611","525","479","420","521","440","0","0","0","0.2409",{"$nulls":20},"3.509258","2.54","2.67","1","-5.38","1.0","0.002","0.726;0.737",{"$nulls":3},"Unknown",-1,{"$nulls":6},"C4283894","0/0","582,0","0","582","0/1","362,129","0.2627","491",null,"chrX:74592201:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2643"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","RPS27A","chr2:55232771","RPS27A(start_lost)",null,null,"domain (Ubiquitin-like )","antibody-mapping:heterologous_protein_expression_evidence, domain:Ubiquitin-like, beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW, LOW, LOW",null,255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.; ",{"$nulls":4},"p.Met1_Phe4delins???","c.-17-36_10delTGACCTAACCTGTCTCTTCCTTTTCCTCAACCTCAGGTGGAGCCGCCACCAAAATGCAGATTTinsGCTCC","HIGH","1/156",2,{"$nulls":20},"55232834",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr2:55232771:CTGACCTAACCTGTCTCTTCCTTTTCCTCAACCTCAGGTGGAGCCGCCACCAAAATGCAGATTT:CGCTCC",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","RPS27A","chr2:55232771","RPS27A(start_lost)",null,null,"domain (Ubiquitin-like )","antibody-mapping:heterologous_protein_expression_evidence, domain:Ubiquitin-like, beta-strand:combinatorial_evidence_used_in_manual_assertion","LOW, LOW, LOW",null,255,"PASS","High Or Moderate Variant",null,-1,null,"FUNCTION: Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.; ",{"$nulls":4},"p.Met1_Phe4delins???","c.-17-36_10delTGACCTAACCTGTCTCTTCCTTTTCCTCAACCTCAGGTGGAGCCGCCACCAAAATGCAGATTTinsGCTCC","HIGH","1/156",2,{"$nulls":20},"55232834",{"$nulls":26},"Unknown",-1,{"$nulls":16},"chr2:55232771:CTGACCTAACCTGTCTCTTCCTTTTCCTCAACCTCAGGTGGAGCCGCCACCAAAATGCAGATTT:CGCTCC",0,0,"smallDeletion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.manta.somaticSV.vcf.gz","structuralVariantFile","PASS","tumor","significant"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","RXFP2","chr13:31761783","RXFP2(A101S)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for relaxin. The activity of this receptor is mediated by G proteins leading to stimulation of adenylate cyclase and an increase of cAMP. May also be a receptor for Leydig insulin-like peptide (INSL3).; ",{"$nulls":4},"p.Ala101Ser","c.301G>T","MODERATE","101/754",3,{"$nulls":5},"4","492","241","311","153","456","204","0.002","0.002","0","0.5588",{"$nulls":20},"1.211508","-0.63;-0.55","1.61","0.999396","-0.23;-0.16",".;0.009","0.402;0.269","0.271;0.143",{"$nulls":3},"Unknown",-1,"AD","Cryptorchidism","Genitourinary",{"$nulls":4},"0/0","476,1","0.0021","477","0/1","99,135","0.5769","234",null,"chr13:31761783:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5686"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","RXFP2","chr13:31761783","RXFP2(A101S)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Receptor for relaxin. The activity of this receptor is mediated by G proteins leading to stimulation of adenylate cyclase and an increase of cAMP. May also be a receptor for Leydig insulin-like peptide (INSL3).; ",{"$nulls":4},"p.Ala101Ser","c.301G>T","MODERATE","101/754",3,{"$nulls":5},"4","492","326","311","206","458","293","0.002","0.002","0","0.3823",{"$nulls":20},"1.211508","-0.63;-0.55","1.61","0.999396","-0.23;-0.16",".;0.009","0.402;0.269","0.271;0.143",{"$nulls":3},"Unknown",-1,"AD","Cryptorchidism","Genitourinary",{"$nulls":4},"0/0","476,1","0.0021","477","0/1","184,127","0.4084","311",null,"chr13:31761783:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3738"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SAMHD1","chr20:36916769","SAMHD1(R339S)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs962672070",-1,"DISEASE: Aicardi-Goutieres syndrome 5 (AGS5) [MIM:612952]: A form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood. {ECO:0000269|PubMed:19525956, ECO:0000269|PubMed:20131292, ECO:0000269|PubMed:20842748, ECO:0000269|PubMed:24035396, ECO:0000269|PubMed:24183309, ECO:0000269|PubMed:28229507, ECO:0000269|PubMed:29670289}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Chilblain lupus 2 (CHBL2) [MIM:614415]: A rare cutaneous form of lupus erythematosus. Affected individuals present with painful bluish-red papular or nodular lesions of the skin in acral locations precipitated by cold and wet exposure at temperatures less than 10 degrees centigrade. {ECO:0000269|PubMed:21204240}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Protein that acts both as a host restriction factor involved in defense response to virus and as a regulator of DNA end resection at stalled replication forks (PubMed:19525956, PubMed:21613998, PubMed:21720370, PubMed:23602554, PubMed:23601106, PubMed:22056990, PubMed:24336198, PubMed:26294762, PubMed:26431200, PubMed:28229507, PubMed:28834754, PubMed:29670289). Has deoxynucleoside triphosphate (dNTPase) activity, which is required to restrict infection by viruses, such as HIV-1: dNTPase activity reduces cellular dNTP levels to levels too low for retroviral reverse transcription to occur, blocking early-stage virus replication in dendritic and other myeloid cells (PubMed:19525956, PubMed:21613998, PubMed:21720370, PubMed:23602554, PubMed:23601106, PubMed:23364794, PubMed:25038827, PubMed:26101257, PubMed:22056990, PubMed:24336198, PubMed:28229507, PubMed:26294762, PubMed:26431200). Likewise, suppresses LINE-1 retrotransposon activity (PubMed:24035396, PubMed:29610582, PubMed:24217394). Not able to restrict infection by HIV-2 virus; because restriction activity is counteracted by HIV-2 viral protein Vpx (PubMed:21613998, PubMed:21720370). In addition to virus restriction, dNTPase activity acts as a regulator of DNA precursor pools by regulating dNTP pools (PubMed:23858451). Phosphorylation at Thr-592 acts as a switch to control dNTPase-dependent and -independent functions: it inhibits dNTPase activity and ability to restrict infection by viruses, while it promotes DNA end resection at stalled replication forks (PubMed:23602554, PubMed:23601106, PubMed:29610582, PubMed:29670289). Functions during S phase at stalled DNA replication forks to promote the resection of gapped or reversed forks: acts by stimulating the exonuclease activity of MRE11, activating the ATR-CHK1 pathway and allowing the forks to restart replication (PubMed:29670289). Its ability to promote degradation of nascent DNA at stalled replication forks is required to prevent induction of type I interferons, thereby preventing chronic inflammation (PubMed:27477283, PubMed:29670289). Ability to promote DNA end resection at stalled replication forks is independent of dNTPase activity (PubMed:29670289). Enhances immunoglobulin hypermutation in B-lymphocytes by promoting transversion mutation (By similarity). {ECO:0000250|UniProtKB:Q60710, ECO:0000269|PubMed:19525956, ECO:0000269|PubMed:21613998, ECO:0000269|PubMed:21720370, ECO:0000269|PubMed:22056990, ECO:0000269|PubMed:23364794, ECO:0000269|PubMed:23601106, ECO:0000269|PubMed:23602554, ECO:0000269|PubMed:23858451, ECO:0000269|PubMed:24035396, ECO:0000269|PubMed:24217394, ECO:0000269|PubMed:24336198, ECO:0000269|PubMed:25038827, ECO:0000269|PubMed:26101257, ECO:0000269|PubMed:26294762, ECO:0000269|PubMed:26431200, ECO:0000269|PubMed:27477283, ECO:0000269|PubMed:28229507, ECO:0000269|PubMed:28834754, ECO:0000269|PubMed:29610582, ECO:0000269|PubMed:29670289}.; ",{"$nulls":5},"c.1015C>A","HIGH",null,9,1,{"$nulls":4},"5","180","185","120","120","154","157","0","0","0","0.1783",{"$nulls":20},"3.753943",".;-3.74;.","3.86;3.86;.","1",".;-5.07;.","0.996;.;.",".;0.001;.",".;0.912;.",{"$nulls":3},"Unknown",-1,"AR","Aicardi-Goutieres syndrome 5","Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Neurologic",{"$nulls":3},"C2749659| C3280721","0/0","171,0","0","171","0/1","141,32","0.185","173",null,"chr20:36916769:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1917"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SAMHD1","chr20:36916769","SAMHD1(R339S)",{"$nulls":6},255,"PASS","High Or Moderate Variant","rs962672070",-1,"DISEASE: Aicardi-Goutieres syndrome 5 (AGS5) [MIM:612952]: A form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood. {ECO:0000269|PubMed:19525956, ECO:0000269|PubMed:20131292, ECO:0000269|PubMed:20842748, ECO:0000269|PubMed:24035396, ECO:0000269|PubMed:24183309, ECO:0000269|PubMed:28229507, ECO:0000269|PubMed:29670289}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Chilblain lupus 2 (CHBL2) [MIM:614415]: A rare cutaneous form of lupus erythematosus. Affected individuals present with painful bluish-red papular or nodular lesions of the skin in acral locations precipitated by cold and wet exposure at temperatures less than 10 degrees centigrade. {ECO:0000269|PubMed:21204240}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Protein that acts both as a host restriction factor involved in defense response to virus and as a regulator of DNA end resection at stalled replication forks (PubMed:19525956, PubMed:21613998, PubMed:21720370, PubMed:23602554, PubMed:23601106, PubMed:22056990, PubMed:24336198, PubMed:26294762, PubMed:26431200, PubMed:28229507, PubMed:28834754, PubMed:29670289). Has deoxynucleoside triphosphate (dNTPase) activity, which is required to restrict infection by viruses, such as HIV-1: dNTPase activity reduces cellular dNTP levels to levels too low for retroviral reverse transcription to occur, blocking early-stage virus replication in dendritic and other myeloid cells (PubMed:19525956, PubMed:21613998, PubMed:21720370, PubMed:23602554, PubMed:23601106, PubMed:23364794, PubMed:25038827, PubMed:26101257, PubMed:22056990, PubMed:24336198, PubMed:28229507, PubMed:26294762, PubMed:26431200). Likewise, suppresses LINE-1 retrotransposon activity (PubMed:24035396, PubMed:29610582, PubMed:24217394). Not able to restrict infection by HIV-2 virus; because restriction activity is counteracted by HIV-2 viral protein Vpx (PubMed:21613998, PubMed:21720370). In addition to virus restriction, dNTPase activity acts as a regulator of DNA precursor pools by regulating dNTP pools (PubMed:23858451). Phosphorylation at Thr-592 acts as a switch to control dNTPase-dependent and -independent functions: it inhibits dNTPase activity and ability to restrict infection by viruses, while it promotes DNA end resection at stalled replication forks (PubMed:23602554, PubMed:23601106, PubMed:29610582, PubMed:29670289). Functions during S phase at stalled DNA replication forks to promote the resection of gapped or reversed forks: acts by stimulating the exonuclease activity of MRE11, activating the ATR-CHK1 pathway and allowing the forks to restart replication (PubMed:29670289). Its ability to promote degradation of nascent DNA at stalled replication forks is required to prevent induction of type I interferons, thereby preventing chronic inflammation (PubMed:27477283, PubMed:29670289). Ability to promote DNA end resection at stalled replication forks is independent of dNTPase activity (PubMed:29670289). Enhances immunoglobulin hypermutation in B-lymphocytes by promoting transversion mutation (By similarity). {ECO:0000250|UniProtKB:Q60710, ECO:0000269|PubMed:19525956, ECO:0000269|PubMed:21613998, ECO:0000269|PubMed:21720370, ECO:0000269|PubMed:22056990, ECO:0000269|PubMed:23364794, ECO:0000269|PubMed:23601106, ECO:0000269|PubMed:23602554, ECO:0000269|PubMed:23858451, ECO:0000269|PubMed:24035396, ECO:0000269|PubMed:24217394, ECO:0000269|PubMed:24336198, ECO:0000269|PubMed:25038827, ECO:0000269|PubMed:26101257, ECO:0000269|PubMed:26294762, ECO:0000269|PubMed:26431200, ECO:0000269|PubMed:27477283, ECO:0000269|PubMed:28229507, ECO:0000269|PubMed:28834754, ECO:0000269|PubMed:29610582, ECO:0000269|PubMed:29670289}.; ",{"$nulls":5},"c.1015C>A","HIGH",null,9,1,{"$nulls":4},"3","180","253","120","171",null,null,"0","0",{"$nulls":22},"3.753943",".;-3.74;.","3.86;3.86;.","1",".;-5.07;.","0.996;.;.",".;0.001;.",".;0.912;.",{"$nulls":3},"Unknown",-1,"AR","Aicardi-Goutieres syndrome 5","Cardiovascular; Dermatologic; Gastrointestinal; Hematologic; Neurologic",{"$nulls":3},"C2749659| C3280721","0/0","167,0","0","167","0/1","217,13","0.0565","230",null,"chr20:36916769:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0585"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SIRT2","chr19:38879301","SIRT2(E342Q)",null,null,"splice variant (In isoform 4. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: NAD-dependent protein deacetylase, which deacetylates internal lysines on histone and alpha-tubulin as well as many other proteins such as key transcription factors (PubMed:24177535, PubMed:12620231, PubMed:16648462, PubMed:18249187, PubMed:18332217, PubMed:18995842, PubMed:20587414, PubMed:21081649, PubMed:20543840, PubMed:22014574, PubMed:21726808, PubMed:21949390, PubMed:22771473, PubMed:23468428, PubMed:23908241, PubMed:24940000, PubMed:24769394, PubMed:24681946). Participates in the modulation of multiple and diverse biological processes such as cell cycle control, genomic integrity, microtubule dynamics, cell differentiation, metabolic networks, and autophagy. Plays a major role in the control of cell cycle progression and genomic stability. Functions in the antephase checkpoint preventing precocious mitotic entry in response to microtubule stress agents, and hence allowing proper inheritance of chromosomes. Positively regulates the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase complex activity by deacetylating CDC20 and FZR1, then allowing progression through mitosis. Associates both with chromatin at transcriptional start sites (TSSs) and enhancers of active genes. Plays a role in cell cycle and chromatin compaction through epigenetic modulation of the regulation of histone H4 'Lys-20' methylation (H4K20me1) during early mitosis. Specifically deacetylates histone H4 at 'Lys-16' (H4K16ac) between the G2/M transition and metaphase enabling H4K20me1 deposition by KMT5A leading to ulterior levels of H4K20me2 and H4K20me3 deposition throughout cell cycle, and mitotic S-phase progression (PubMed:23468428). Deacetylates KMT5A modulating KMT5A chromatin localization during the mitotic stress response (PubMed:23468428). Deacetylates also histone H3 at 'Lys-57' (H3K56ac) during the mitotic G2/M transition. Upon bacterium Listeria monocytogenes infection, deacetylates 'Lys-18' of histone H3 in a receptor tyrosine kinase MET- and PI3K/Akt-dependent manner, thereby inhibiting transcriptional activity and promoting late stages of listeria infection (PubMed:23908241). During oocyte meiosis progression, may deacetylate histone H4 at 'Lys-16' (H4K16ac) and alpha-tubulin, regulating spindle assembly and chromosome alignment by influencing microtubule dynamics and kinetochore function. Deacetylates histone H4 at 'Lys-16' (H4K16ac) at the VEGFA promoter and thereby contributes to regulate expression of VEGFA, a key regulator of angiogenesis (PubMed:24940000). Deacetylates alpha-tubulin at 'Lys-40' and hence controls neuronal motility, oligodendroglial cell arbor projection processes and proliferation of non-neuronal cells. Phosphorylation at Ser-368 by a G1/S-specific cyclin E-CDK2 complex inactivates SIRT2-mediated alpha-tubulin deacetylation, negatively regulating cell adhesion, cell migration and neurite outgrowth during neuronal differentiation. Deacetylates PARD3 and participates in the regulation of Schwann cell peripheral myelination formation during early postnatal development and during postinjury remyelination. Involved in several cellular metabolic pathways. Plays a role in the regulation of blood glucose homeostasis by deacetylating and stabilizing phosphoenolpyruvate carboxykinase PCK1 activity in response to low nutrient availability. Acts as a key regulator in the pentose phosphate pathway (PPP) by deacetylating and activating the glucose-6-phosphate G6PD enzyme, and therefore, stimulates the production of cytosolic NADPH to counteract oxidative damage. Maintains energy homeostasis in response to nutrient deprivation as well as energy expenditure by inhibiting adipogenesis and promoting lipolysis. Attenuates adipocyte differentiation by deacetylating and promoting FOXO1 interaction to PPARG and subsequent repression of PPARG-dependent transcriptional activity. Plays a role in the regulation of lysosome-mediated degradation of protein aggregates by autophagy in neuronal cells. Deacetylates FOXO1 in response to oxidative stress or serum deprivation, thereby negatively regulating FOXO1- mediated autophagy (PubMed:20543840). Deacetylates a broad range of transcription factors and co-regulators regulating target gene expression. Deacetylates transcriptional factor FOXO3 stimulating the ubiquitin ligase SCF(SKP2)-mediated FOXO3 ubiquitination and degradation (By similarity). Deacetylates HIF1A and therefore promotes HIF1A degradation and inhibition of HIF1A transcriptional activity in tumor cells in response to hypoxia (PubMed:24681946). Deacetylates RELA in the cytoplasm inhibiting NF-kappaB-dependent transcription activation upon TNF-alpha stimulation. Inhibits transcriptional activation by deacetylating p53/TP53 and EP300 (PubMed:18249187). Deacetylates also EIF5A (PubMed:22771473). Functions as a negative regulator on oxidative stress-tolerance in response to anoxia-reoxygenation conditions. Plays a role as tumor suppressor (PubMed:22014574). {ECO:0000250|UniProtKB:Q8VDQ8, ECO:0000269|PubMed:12620231, ECO:0000269|PubMed:12697818, ECO:0000269|PubMed:16648462, ECO:0000269|PubMed:16909107, ECO:0000269|PubMed:17488717, ECO:0000269|PubMed:17574768, ECO:0000269|PubMed:17726514, ECO:0000269|PubMed:18249187, ECO:0000269|PubMed:18332217, ECO:0000269|PubMed:18640115, ECO:0000269|PubMed:18722353, ECO:0000269|PubMed:18995842, ECO:0000269|PubMed:19282667, ECO:0000269|PubMed:20543840, ECO:0000269|PubMed:20587414, ECO:0000269|PubMed:21081649, ECO:0000269|PubMed:21726808, ECO:0000269|PubMed:21949390, ECO:0000269|PubMed:22014574, ECO:0000269|PubMed:22771473, ECO:0000269|PubMed:22819792, ECO:0000269|PubMed:23468428, ECO:0000269|PubMed:23908241, ECO:0000269|PubMed:23932781, ECO:0000269|PubMed:24177535, ECO:0000269|PubMed:24681946, ECO:0000269|PubMed:24769394, ECO:0000269|PubMed:24940000}.; FUNCTION: Isoform 2: Deacetylates EP300, alpha-tubulin and histone H3 and H4. {ECO:0000269|PubMed:24177535}.; ",{"$nulls":4},"p.Glu342Gln","c.1024G>C","MODERATE","342/389",16,{"$nulls":5},"5","430","241","344","190","340","207","0","0","0","0.5797",{"$nulls":20},"2.64831","2.25;2.25;.","1.53;.;.","0.999114;1","-0.31;-0.31;.","0.006;0.01;.","0.394;0.443;.","0.114;0.119;0.298",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","412,0","0","412","0/1","108,129","0.5443","237",null,"chr19:38879301:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5684"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SIRT2","chr19:38879301","SIRT2(E342Q)",null,null,"splice variant (In isoform 4. ), helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: NAD-dependent protein deacetylase, which deacetylates internal lysines on histone and alpha-tubulin as well as many other proteins such as key transcription factors (PubMed:24177535, PubMed:12620231, PubMed:16648462, PubMed:18249187, PubMed:18332217, PubMed:18995842, PubMed:20587414, PubMed:21081649, PubMed:20543840, PubMed:22014574, PubMed:21726808, PubMed:21949390, PubMed:22771473, PubMed:23468428, PubMed:23908241, PubMed:24940000, PubMed:24769394, PubMed:24681946). Participates in the modulation of multiple and diverse biological processes such as cell cycle control, genomic integrity, microtubule dynamics, cell differentiation, metabolic networks, and autophagy. Plays a major role in the control of cell cycle progression and genomic stability. Functions in the antephase checkpoint preventing precocious mitotic entry in response to microtubule stress agents, and hence allowing proper inheritance of chromosomes. Positively regulates the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase complex activity by deacetylating CDC20 and FZR1, then allowing progression through mitosis. Associates both with chromatin at transcriptional start sites (TSSs) and enhancers of active genes. Plays a role in cell cycle and chromatin compaction through epigenetic modulation of the regulation of histone H4 'Lys-20' methylation (H4K20me1) during early mitosis. Specifically deacetylates histone H4 at 'Lys-16' (H4K16ac) between the G2/M transition and metaphase enabling H4K20me1 deposition by KMT5A leading to ulterior levels of H4K20me2 and H4K20me3 deposition throughout cell cycle, and mitotic S-phase progression (PubMed:23468428). Deacetylates KMT5A modulating KMT5A chromatin localization during the mitotic stress response (PubMed:23468428). Deacetylates also histone H3 at 'Lys-57' (H3K56ac) during the mitotic G2/M transition. Upon bacterium Listeria monocytogenes infection, deacetylates 'Lys-18' of histone H3 in a receptor tyrosine kinase MET- and PI3K/Akt-dependent manner, thereby inhibiting transcriptional activity and promoting late stages of listeria infection (PubMed:23908241). During oocyte meiosis progression, may deacetylate histone H4 at 'Lys-16' (H4K16ac) and alpha-tubulin, regulating spindle assembly and chromosome alignment by influencing microtubule dynamics and kinetochore function. Deacetylates histone H4 at 'Lys-16' (H4K16ac) at the VEGFA promoter and thereby contributes to regulate expression of VEGFA, a key regulator of angiogenesis (PubMed:24940000). Deacetylates alpha-tubulin at 'Lys-40' and hence controls neuronal motility, oligodendroglial cell arbor projection processes and proliferation of non-neuronal cells. Phosphorylation at Ser-368 by a G1/S-specific cyclin E-CDK2 complex inactivates SIRT2-mediated alpha-tubulin deacetylation, negatively regulating cell adhesion, cell migration and neurite outgrowth during neuronal differentiation. Deacetylates PARD3 and participates in the regulation of Schwann cell peripheral myelination formation during early postnatal development and during postinjury remyelination. Involved in several cellular metabolic pathways. Plays a role in the regulation of blood glucose homeostasis by deacetylating and stabilizing phosphoenolpyruvate carboxykinase PCK1 activity in response to low nutrient availability. Acts as a key regulator in the pentose phosphate pathway (PPP) by deacetylating and activating the glucose-6-phosphate G6PD enzyme, and therefore, stimulates the production of cytosolic NADPH to counteract oxidative damage. Maintains energy homeostasis in response to nutrient deprivation as well as energy expenditure by inhibiting adipogenesis and promoting lipolysis. Attenuates adipocyte differentiation by deacetylating and promoting FOXO1 interaction to PPARG and subsequent repression of PPARG-dependent transcriptional activity. Plays a role in the regulation of lysosome-mediated degradation of protein aggregates by autophagy in neuronal cells. Deacetylates FOXO1 in response to oxidative stress or serum deprivation, thereby negatively regulating FOXO1- mediated autophagy (PubMed:20543840). Deacetylates a broad range of transcription factors and co-regulators regulating target gene expression. Deacetylates transcriptional factor FOXO3 stimulating the ubiquitin ligase SCF(SKP2)-mediated FOXO3 ubiquitination and degradation (By similarity). Deacetylates HIF1A and therefore promotes HIF1A degradation and inhibition of HIF1A transcriptional activity in tumor cells in response to hypoxia (PubMed:24681946). Deacetylates RELA in the cytoplasm inhibiting NF-kappaB-dependent transcription activation upon TNF-alpha stimulation. Inhibits transcriptional activation by deacetylating p53/TP53 and EP300 (PubMed:18249187). Deacetylates also EIF5A (PubMed:22771473). Functions as a negative regulator on oxidative stress-tolerance in response to anoxia-reoxygenation conditions. Plays a role as tumor suppressor (PubMed:22014574). {ECO:0000250|UniProtKB:Q8VDQ8, ECO:0000269|PubMed:12620231, ECO:0000269|PubMed:12697818, ECO:0000269|PubMed:16648462, ECO:0000269|PubMed:16909107, ECO:0000269|PubMed:17488717, ECO:0000269|PubMed:17574768, ECO:0000269|PubMed:17726514, ECO:0000269|PubMed:18249187, ECO:0000269|PubMed:18332217, ECO:0000269|PubMed:18640115, ECO:0000269|PubMed:18722353, ECO:0000269|PubMed:18995842, ECO:0000269|PubMed:19282667, ECO:0000269|PubMed:20543840, ECO:0000269|PubMed:20587414, ECO:0000269|PubMed:21081649, ECO:0000269|PubMed:21726808, ECO:0000269|PubMed:21949390, ECO:0000269|PubMed:22014574, ECO:0000269|PubMed:22771473, ECO:0000269|PubMed:22819792, ECO:0000269|PubMed:23468428, ECO:0000269|PubMed:23908241, ECO:0000269|PubMed:23932781, ECO:0000269|PubMed:24177535, ECO:0000269|PubMed:24681946, ECO:0000269|PubMed:24769394, ECO:0000269|PubMed:24940000}.; FUNCTION: Isoform 2: Deacetylates EP300, alpha-tubulin and histone H3 and H4. {ECO:0000269|PubMed:24177535}.; ",{"$nulls":4},"p.Glu342Gln","c.1024G>C","MODERATE","342/389",16,{"$nulls":5},"5","430","314","344","243","343","252","0","0","0","0.4524",{"$nulls":20},"2.64831","2.25;2.25;.","1.53;.;.","0.999114;1","-0.31;-0.31;.","0.006;0.01;.","0.394;0.443;.","0.114;0.119;0.298",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","413,0","0","413","0/1","161,138","0.4615","299",null,"chr19:38879301:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4444"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SLAMF6","chr1:160489150","SLAMF6(E273K)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs768630969",1.499E-5,null,"FUNCTION: Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Triggers cytolytic activity only in natural killer cells (NK) expressing high surface densities of natural cytotoxicity receptors (PubMed:11489943, PubMed:16920955). Positive signaling in NK cells implicates phosphorylation of VAV1. NK cell activation seems to depend on SH2D1B and not on SH2D1A (PubMed:16920955). In conjunction with SLAMF1 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage (By similarity). Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727, PubMed:16920955). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). In conjunction with SLAMF1 and CD84/SLAMF5 may be a negative regulator of the humoral immune response. In the absence of SH2D1A/SAP can transmit negative signals to CD4(+) T-cells and NKT cells. Negatively regulates germinal center formation by inhibiting T-cell:B-cell adhesion; the function probably implicates increased association with PTPN6/SHP-1 via ITSMs in absence of SH2D1A/SAP. However, reported to be involved in maintaining B-cell tolerance in germinal centers and in preventing autoimmunity (By similarity). {ECO:0000250|UniProtKB:Q9ET39, ECO:0000269|PubMed:11489943, ECO:0000269|PubMed:16920955, ECO:0000269|PubMed:22184727, ECO:0000269|PubMed:22989874}.; ",{"$nulls":4},"p.Glu273Lys","c.817G>A","MODERATE","273/332",6,{"$nulls":5},"5","541","443","368","309","477","386","0","0","0","0.3316",{"$nulls":20},"2.316649","2.83;2.84;2.21",".;0.755;.","1","-1.57;-1.47;-1.43",".;0.906;.","0.083;0.047;0.025","0.328;0.307;0.323",{"$nulls":3},"ExAC_NFE_AF",1.499E-5,{"$nulls":7},"0/0","530,0","0","530","0/1","297,140","0.3204","437",null,"chr1:160489150:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3398"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SLAMF6","chr1:160489150","SLAMF6(E273K)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Missense","rs768630969",1.499E-5,null,"FUNCTION: Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Triggers cytolytic activity only in natural killer cells (NK) expressing high surface densities of natural cytotoxicity receptors (PubMed:11489943, PubMed:16920955). Positive signaling in NK cells implicates phosphorylation of VAV1. NK cell activation seems to depend on SH2D1B and not on SH2D1A (PubMed:16920955). In conjunction with SLAMF1 controls the transition between positive selection and the subsequent expansion and differentiation of the thymocytic natural killer T (NKT) cell lineage (By similarity). Promotes T-cell differentiation into a helper T-cell Th17 phenotype leading to increased IL-17 secretion; the costimulatory activity requires SH2D1A (PubMed:22184727, PubMed:16920955). Promotes recruitment of RORC to the IL-17 promoter (PubMed:22989874). In conjunction with SLAMF1 and CD84/SLAMF5 may be a negative regulator of the humoral immune response. In the absence of SH2D1A/SAP can transmit negative signals to CD4(+) T-cells and NKT cells. Negatively regulates germinal center formation by inhibiting T-cell:B-cell adhesion; the function probably implicates increased association with PTPN6/SHP-1 via ITSMs in absence of SH2D1A/SAP. However, reported to be involved in maintaining B-cell tolerance in germinal centers and in preventing autoimmunity (By similarity). {ECO:0000250|UniProtKB:Q9ET39, ECO:0000269|PubMed:11489943, ECO:0000269|PubMed:16920955, ECO:0000269|PubMed:22184727, ECO:0000269|PubMed:22989874}.; ",{"$nulls":4},"p.Glu273Lys","c.817G>A","MODERATE","273/332",6,{"$nulls":5},"5","541","503","368","360","478","431","0","0","0","0.4246",{"$nulls":20},"2.316649","2.83;2.84;2.21",".;0.755;.","1","-1.57;-1.47;-1.43",".;0.906;.","0.083;0.047;0.025","0.328;0.307;0.323",{"$nulls":3},"ExAC_NFE_AF",1.499E-5,{"$nulls":7},"0/0","530,0","0","530","0/1","281,205","0.4218","486",null,"chr1:160489150:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4222"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SLC24A2","chr9:19786662","SLC24A2(E69K)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Critical component of the visual transduction cascade, controlling the calcium concentration of outer segments during light and darkness. Light causes a rapid lowering of cytosolic free calcium in the outer segment of both retinal rod and cone photoreceptors and the light-induced lowering of calcium is caused by extrusion via this protein which plays a key role in the process of light adaptation. Transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).; ",{"$nulls":4},"p.Glu69Lys","c.205G>A","MODERATE","69/661",1,{"$nulls":5},"4","427","332","316","261","381","294","0","0","0","0.2993",{"$nulls":20},"1.746462","-0.86","1.78","1","-0.83;-0.87","0.031;0.052","0.149;0.16","0.201;0.224",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","415,0","0","415","0/1","229,98","0.2997","327",null,"chr9:19786662:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.295"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SLC9A5","chr16:67259911","SLC9A5(L603V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient. Plays an important role in signal transduction (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu603Val","c.1807C>G","MODERATE","603/896",12,{"$nulls":5},"4","461","420","304","278","426","366","0","0","0","0.3251",{"$nulls":20},"1.750905","-0.06;0.38;.",".;0.155;.","0.790267",".;-1.47;.",".;0.001;.",".;0.292;.",".;0.187;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","439,0","0","439","0/1","258,145","0.3598","403",null,"chr16:67259911:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3525"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SLC9A5","chr16:67259911","SLC9A5(L603V)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient. Plays an important role in signal transduction (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Leu603Val","c.1807C>G","MODERATE","603/896",12,{"$nulls":5},"4","461","491","304","319","426","445","0","0","0","0.3326",{"$nulls":20},"1.750905","-0.06;0.38;.",".;0.155;.","0.790267",".;-1.47;.",".;0.001;.",".;0.292;.",".;0.187;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","439,0","0","439","0/1","309,158","0.3383","467",null,"chr16:67259911:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3041"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SLC9A5","chr16:67270885","SLC9A5(T789M)",{"$nulls":6},255,"PASS","Missense","rs755495387",1.656e-05,null,"FUNCTION: Involved in pH regulation to eliminate acids generated by active metabolism or to counter adverse environmental conditions. Major proton extruding system driven by the inward sodium ion chemical gradient. Plays an important role in signal transduction (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Thr789Met","c.2366C>T","MODERATE","789/896",16,1,{"$nulls":4},"4","395","354","282","269","326","312","0","0","0","0.0513",{"$nulls":20},"1.287194","0.5",null,"0.999254","-0.27","0.003","0.02","0.031",{"$nulls":3},"ExAC_Adj_AF",1.656e-05,{"$nulls":7},"0/0","377,0","0","377","0/1","324,18","0.0526","342",null,"chr16:67270885:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.0558"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SORCS3","chr10:105263336","SORCS3(E1211*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Glu1211*","c.3631G>T","HIGH","1211/1222",28,1,{"$nulls":4},"4","287","298","204","208","230","229","0","0","0","0.2926",{"$nulls":20},"8.711794",null,null,"1",{"$nulls":3},"0.299;0.302",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","285,0","0","285","0/1","207,83","0.2862","290",null,"chr10:105263336:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2837"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SORCS3","chr10:105263336","SORCS3(E1211*)",null,null,"topological domain (Cytoplasmic )",{"$nulls":3},255,"PASS","Loss Of Function",null,-1,{"$nulls":6},"p.Glu1211*","c.3631G>T","HIGH","1211/1222",28,1,{"$nulls":4},"4","287","272","204","195","230","227","0","0","0","0.2115",{"$nulls":20},"8.711794",null,null,"1",{"$nulls":3},"0.299;0.302",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","285,0","0","285","0/1","214,53","0.1985","267",null,"chr10:105263336:G:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1897"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","STAB2","chr12:103640136","STAB2(C307Y)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs755546166",1.501E-5,null,"FUNCTION: Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Hyaluronan receptor that binds to and mediates endocytosis of hyaluronic acid (HA). Acts also, in different species, as a primary systemic scavenger receptor for heparin (Hep), chondroitin sulfate (CS), dermatan sulfate (DS), nonglycosaminoglycan (GAG), acetylated low-density lipoprotein (AcLDL), pro-collagen propeptides and advanced glycation end products (AGE). May serve to maintain tissue integrity by supporting extracellular matrix turnover or it may contribute to maintaining fluidity of bodily liquids by resorption of hyaluronan. Counter receptor which plays an important role in lymphocyte recruitment in the hepatic vasculature. Binds to both Gram-positive and Gram-negative bacteria and may play a role in defense against bacterial infection. The proteolytically processed 190 kDa form also functions as an endocytosis receptor for heparin internalisation as well as HA and CS. {ECO:0000269|PubMed:12077138, ECO:0000269|PubMed:12473645, ECO:0000269|PubMed:15208308, ECO:0000269|PubMed:15572036, ECO:0000269|PubMed:17145755, ECO:0000269|PubMed:17675564, ECO:0000269|PubMed:17962816, ECO:0000269|PubMed:18230608, ECO:0000269|PubMed:18434317, ECO:0000269|PubMed:18573870, ECO:0000269|PubMed:19359419}.; ",{"$nulls":4},"p.Cys307Tyr","c.920G>A","MODERATE","307/2551",9,{"$nulls":5},"5","329","301","253","228","280","253","0","0","0","0.3478",{"$nulls":20},"3.801551","-1.44","4.22","0.99993","-9.3","1.0",null,"0.942",{"$nulls":3},"ExAC_NFE_AF",1.501E-5,{"$nulls":7},"0/0","326,0","0","326","0/1","193,102","0.3458","295",null,"chr12:103640136:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3377"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","STAB2","chr12:103640136","STAB2(C307Y)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs755546166",1.501E-5,null,"FUNCTION: Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Hyaluronan receptor that binds to and mediates endocytosis of hyaluronic acid (HA). Acts also, in different species, as a primary systemic scavenger receptor for heparin (Hep), chondroitin sulfate (CS), dermatan sulfate (DS), nonglycosaminoglycan (GAG), acetylated low-density lipoprotein (AcLDL), pro-collagen propeptides and advanced glycation end products (AGE). May serve to maintain tissue integrity by supporting extracellular matrix turnover or it may contribute to maintaining fluidity of bodily liquids by resorption of hyaluronan. Counter receptor which plays an important role in lymphocyte recruitment in the hepatic vasculature. Binds to both Gram-positive and Gram-negative bacteria and may play a role in defense against bacterial infection. The proteolytically processed 190 kDa form also functions as an endocytosis receptor for heparin internalisation as well as HA and CS. {ECO:0000269|PubMed:12077138, ECO:0000269|PubMed:12473645, ECO:0000269|PubMed:15208308, ECO:0000269|PubMed:15572036, ECO:0000269|PubMed:17145755, ECO:0000269|PubMed:17675564, ECO:0000269|PubMed:17962816, ECO:0000269|PubMed:18230608, ECO:0000269|PubMed:18434317, ECO:0000269|PubMed:18573870, ECO:0000269|PubMed:19359419}.; ",{"$nulls":4},"p.Cys307Tyr","c.920G>A","MODERATE","307/2551",9,{"$nulls":5},"5","329","349","253","264","280","271","0","0","0","0.2251",{"$nulls":20},"3.801551","-1.44","4.22","0.99993","-9.3","1.0",null,"0.942",{"$nulls":3},"ExAC_NFE_AF",1.501E-5,{"$nulls":7},"0/0","327,0","0","327","0/1","272,72","0.2093","344",null,"chr12:103640136:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2121"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","STK11","chr19:1221976","STK11(R297T)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Peutz-Jeghers syndrome (PJS) [MIM:175200]: An autosomal dominant disorder characterized by melanocytic macules of the lips, multiple gastrointestinal hamartomatous polyps and an increased risk for various neoplasms, including gastrointestinal cancer. {ECO:0000269|PubMed:10408777, ECO:0000269|PubMed:12372054, ECO:0000269|PubMed:15987703, ECO:0000269|PubMed:21411391, ECO:0000269|PubMed:9425897, ECO:0000269|PubMed:9428765, ECO:0000269|PubMed:9760200, ECO:0000269|PubMed:9837816}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:9605748, ECO:0000269|PubMed:9887330}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Note=Defects in STK11 are associated with some sporadic cancers, especially lung cancers. Frequently mutated and inactivated in non-small cell lung cancer (NSCLC). Defects promote lung cancerigenesis process, especially lung cancer progression and metastasis. Confers lung adenocarcinoma the ability to trans- differentiate into squamous cell carcinoma. Also able to promotes lung cancer metastasis, via both cancer-cell autonomous and non- cancer-cell autonomous mechanisms.; ","FUNCTION: Tumor suppressor serine/threonine-protein kinase that controls the activity of AMP-activated protein kinase (AMPK) family members, thereby playing a role in various processes such as cell metabolism, cell polarity, apoptosis and DNA damage response. Acts by phosphorylating the T-loop of AMPK family proteins, thus promoting their activity: phosphorylates PRKAA1, PRKAA2, BRSK1, BRSK2, MARK1, MARK2, MARK3, MARK4, NUAK1, NUAK2, SIK1, SIK2, SIK3 and SNRK but not MELK. Also phosphorylates non- AMPK family proteins such as STRADA, PTEN and possibly p53/TP53. Acts as a key upstream regulator of AMPK by mediating phosphorylation and activation of AMPK catalytic subunits PRKAA1 and PRKAA2 and thereby regulates processes including: inhibition of signaling pathways that promote cell growth and proliferation when energy levels are low, glucose homeostasis in liver, activation of autophagy when cells undergo nutrient deprivation, and B-cell differentiation in the germinal center in response to DNA damage. Also acts as a regulator of cellular polarity by remodeling the actin cytoskeleton. Required for cortical neuron polarization by mediating phosphorylation and activation of BRSK1 and BRSK2, leading to axon initiation and specification. Involved in DNA damage response: interacts with p53/TP53 and recruited to the CDKN1A/WAF1 promoter to participate in transcription activation. Able to phosphorylate p53/TP53; the relevance of such result in vivo is however unclear and phosphorylation may be indirect and mediated by downstream STK11/LKB1 kinase NUAK1. Also acts as a mediator of p53/TP53-dependent apoptosis via interaction with p53/TP53: translocates to the mitochondrion during apoptosis and regulates p53/TP53-dependent apoptosis pathways. In vein endothelial cells, inhibits PI3K/Akt signaling activity and thus induces apoptosis in response to the oxidant peroxynitrite (in vitro). Regulates UV radiation-induced DNA damage response mediated by CDKN1A. In association with NUAK1, phosphorylates CDKN1A in response to UV radiation and contributes to its degradation which is necessary for optimal DNA repair (PubMed:25329316). {ECO:0000269|PubMed:11430832, ECO:0000269|PubMed:12805220, ECO:0000269|PubMed:14517248, ECO:0000269|PubMed:14976552, ECO:0000269|PubMed:15016379, ECO:0000269|PubMed:15733851, ECO:0000269|PubMed:15987703, ECO:0000269|PubMed:17108107, ECO:0000269|PubMed:18321849, ECO:0000269|PubMed:21317932, ECO:0000269|PubMed:25329316}.; ","acmg|gedi|foundationOne|illumina|ion|level2","[ \"Bosutinib\" , \"Dasatinib\" , \"Everolimus\" , \"Metformin\" , \"Temsirolimus\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Everolimus\" , \"Metformin\" , \"Temsirolimus\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Everolimus\" , \"Metformin\" , \"Temsirolimus\"]",null,"c.890G>C","HIGH",null,7,{"$nulls":5},"4","345","204","241","139","294","173","0","0","0","0.5723",{"$nulls":20},"4.066046",".;-4.15",".;4.415","1",".;-5.61",".;1.0",".;0.001","0.722;0.717",{"$nulls":3},"Unknown",-1,"AD","Peutz-Jeghers syndrome","Dermatologic; Gastrointestinal; Oncologic","COSMIC,kMTOR,vpi3k","This gene, which encodes a member of the serine/threonine kinase family, regulates cell polarity and functions as a tumor suppressor. Mutations in this gene have been associated with Peutz-Jeghers syndrome, an autosomal dominant disorder characterized by the growth of polyps in the gastrointestinal tract, pigmented macules on the skin and mouth, and other neoplasms. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008].  ",null,"C0235974| C0031269| C0153594","0/0","324,0","0","324","0/1","82,105","0.5615","187",null,"chr19:1221976:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5396"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","STK11","chr19:1221976","STK11(R297T)",{"$nulls":6},255,"PASS","High Or Moderate Variant",null,-1,"DISEASE: Peutz-Jeghers syndrome (PJS) [MIM:175200]: An autosomal dominant disorder characterized by melanocytic macules of the lips, multiple gastrointestinal hamartomatous polyps and an increased risk for various neoplasms, including gastrointestinal cancer. {ECO:0000269|PubMed:10408777, ECO:0000269|PubMed:12372054, ECO:0000269|PubMed:15987703, ECO:0000269|PubMed:21411391, ECO:0000269|PubMed:9425897, ECO:0000269|PubMed:9428765, ECO:0000269|PubMed:9760200, ECO:0000269|PubMed:9837816}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Testicular germ cell tumor (TGCT) [MIM:273300]: A common malignancy in males representing 95% of all testicular neoplasms. TGCTs have various pathologic subtypes including: unclassified intratubular germ cell neoplasia, seminoma (including cases with syncytiotrophoblastic cells), spermatocytic seminoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma. {ECO:0000269|PubMed:9605748, ECO:0000269|PubMed:9887330}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Note=Defects in STK11 are associated with some sporadic cancers, especially lung cancers. Frequently mutated and inactivated in non-small cell lung cancer (NSCLC). Defects promote lung cancerigenesis process, especially lung cancer progression and metastasis. Confers lung adenocarcinoma the ability to trans- differentiate into squamous cell carcinoma. Also able to promotes lung cancer metastasis, via both cancer-cell autonomous and non- cancer-cell autonomous mechanisms.; ","FUNCTION: Tumor suppressor serine/threonine-protein kinase that controls the activity of AMP-activated protein kinase (AMPK) family members, thereby playing a role in various processes such as cell metabolism, cell polarity, apoptosis and DNA damage response. Acts by phosphorylating the T-loop of AMPK family proteins, thus promoting their activity: phosphorylates PRKAA1, PRKAA2, BRSK1, BRSK2, MARK1, MARK2, MARK3, MARK4, NUAK1, NUAK2, SIK1, SIK2, SIK3 and SNRK but not MELK. Also phosphorylates non- AMPK family proteins such as STRADA, PTEN and possibly p53/TP53. Acts as a key upstream regulator of AMPK by mediating phosphorylation and activation of AMPK catalytic subunits PRKAA1 and PRKAA2 and thereby regulates processes including: inhibition of signaling pathways that promote cell growth and proliferation when energy levels are low, glucose homeostasis in liver, activation of autophagy when cells undergo nutrient deprivation, and B-cell differentiation in the germinal center in response to DNA damage. Also acts as a regulator of cellular polarity by remodeling the actin cytoskeleton. Required for cortical neuron polarization by mediating phosphorylation and activation of BRSK1 and BRSK2, leading to axon initiation and specification. Involved in DNA damage response: interacts with p53/TP53 and recruited to the CDKN1A/WAF1 promoter to participate in transcription activation. Able to phosphorylate p53/TP53; the relevance of such result in vivo is however unclear and phosphorylation may be indirect and mediated by downstream STK11/LKB1 kinase NUAK1. Also acts as a mediator of p53/TP53-dependent apoptosis via interaction with p53/TP53: translocates to the mitochondrion during apoptosis and regulates p53/TP53-dependent apoptosis pathways. In vein endothelial cells, inhibits PI3K/Akt signaling activity and thus induces apoptosis in response to the oxidant peroxynitrite (in vitro). Regulates UV radiation-induced DNA damage response mediated by CDKN1A. In association with NUAK1, phosphorylates CDKN1A in response to UV radiation and contributes to its degradation which is necessary for optimal DNA repair (PubMed:25329316). {ECO:0000269|PubMed:11430832, ECO:0000269|PubMed:12805220, ECO:0000269|PubMed:14517248, ECO:0000269|PubMed:14976552, ECO:0000269|PubMed:15016379, ECO:0000269|PubMed:15733851, ECO:0000269|PubMed:15987703, ECO:0000269|PubMed:17108107, ECO:0000269|PubMed:18321849, ECO:0000269|PubMed:21317932, ECO:0000269|PubMed:25329316}.; ","acmg|gedi|foundationOne|illumina|ion|level2","[ \"Bosutinib\" , \"Dasatinib\" , \"Everolimus\" , \"Metformin\" , \"Temsirolimus\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Everolimus\" , \"Metformin\" , \"Temsirolimus\"]","[ \"Bosutinib\" , \"Dasatinib\" , \"Everolimus\" , \"Metformin\" , \"Temsirolimus\"]",null,"c.890G>C","HIGH",null,7,{"$nulls":5},"4","345","274","241","185","294","239","0","0","0","0.4184",{"$nulls":20},"4.066046",".;-4.15",".;4.415","1",".;-5.61",".;1.0",".;0.001","0.722;0.717",{"$nulls":3},"Unknown",-1,"AD","Peutz-Jeghers syndrome","Dermatologic; Gastrointestinal; Oncologic","COSMIC,kMTOR,vpi3k","This gene, which encodes a member of the serine/threonine kinase family, regulates cell polarity and functions as a tumor suppressor. Mutations in this gene have been associated with Peutz-Jeghers syndrome, an autosomal dominant disorder characterized by the growth of polyps in the gastrointestinal tract, pigmented macules on the skin and mouth, and other neoplasms. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008].  ",null,"C0235974| C0031269| C0153594","0/0","324,0","0","324","0/1","145,112","0.4358","257",null,"chr19:1221976:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SYN2","chr3:12004757","SYN2(P72_A73insVPQP)",{"$nulls":6},255,"PASS","Inframe Indel","rs1300822093",-1,"DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:15449241}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; ","FUNCTION: Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. May play a role in noradrenaline secretion by sympathetic neurons (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro72_Ala73insValProGlnPro","c.217_218insTGCCGCAGCCCG","MODERATE","73/582",1,{"$nulls":5},"4","63","27","51","27",null,null,"0","0",{"$nulls":33},"Unknown",-1,{"$nulls":4},"This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014].",null,"C0036341","0/0","56,0","0","56","0/1","13,16","0.5517","29",null,"chr3:12004757:C:CGCCGCAGCCCGT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5556"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SYN2","chr3:12004757","SYN2(P72_A73insVPQP)",{"$nulls":6},255,"PASS","Inframe Indel","rs1300822093",-1,"DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:15449241}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.; ","FUNCTION: Neuronal phosphoprotein that coats synaptic vesicles, binds to the cytoskeleton, and is believed to function in the regulation of neurotransmitter release. May play a role in noradrenaline secretion by sympathetic neurons (By similarity). {ECO:0000250}.; ",{"$nulls":4},"p.Pro72_Ala73insValProGlnPro","c.217_218insTGCCGCAGCCCG","MODERATE","73/582",1,{"$nulls":5},"3",null,null,"51","38",{"$nulls":37},"Unknown",-1,{"$nulls":4},"This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014].",null,"C0036341","0/0","56,0","0","56","0/1","25,15","0.375","40",null,"chr3:12004757:C:CGCCGCAGCCCGT",0,0,"smallInsertion","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3947"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","SYNC","chr1:32684064","SYNC(E462K)",null,null,"domain (IF rod ), region of interest (Tail ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Atypical type III intermediate filament (IF) protein that may play a supportive role in the efficient coupling of mechanical stress between the myofibril and fiber exterior. May facilitate lateral force transmission during skeletal muscle contraction. Does not form homofilaments nor heterofilaments with other IF proteins. {ECO:0000250|UniProtKB:Q9EPM5}.; ",{"$nulls":4},"p.Glu462Lys","c.1384G>A","MODERATE","462/482",4,{"$nulls":5},"5","612","311","401","204","567","277","0","0","0","0.5884",{"$nulls":20},"2.949167","-3.76","1.04","1;0.951985","-0.45","0.295","0.019","0.527",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the intermediate filament family which contains an N-terminal head domain, followed by a central coiled-coil region and a short C-terminal tail. The protein is highly expressed in skeletal and cardiac muscle. The protein links the dystrophin associated protein complex (DAPC) to desmin filaments in muscle and may have a structural role in striated muscle. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009].",null,null,"0/0","571,0","0","571","0/1","119,172","0.5911","291",null,"chr1:32684064:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.5784"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","SYNC","chr1:32684064","SYNC(E462K)",null,null,"domain (IF rod ), region of interest (Tail ), splice variant (In isoform 2. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Atypical type III intermediate filament (IF) protein that may play a supportive role in the efficient coupling of mechanical stress between the myofibril and fiber exterior. May facilitate lateral force transmission during skeletal muscle contraction. Does not form homofilaments nor heterofilaments with other IF proteins. {ECO:0000250|UniProtKB:Q9EPM5}.; ",{"$nulls":4},"p.Glu462Lys","c.1384G>A","MODERATE","462/482",4,{"$nulls":5},"5","612","457","401","291","568","407","0","0","0","0.4447",{"$nulls":20},"2.949167","-3.76","1.04","1;0.951985","-0.45","0.295","0.019","0.527",{"$nulls":3},"Unknown",-1,{"$nulls":4},"This gene encodes a member of the intermediate filament family which contains an N-terminal head domain, followed by a central coiled-coil region and a short C-terminal tail. The protein is highly expressed in skeletal and cardiac muscle. The protein links the dystrophin associated protein complex (DAPC) to desmin filaments in muscle and may have a structural role in striated muscle. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009].",null,null,"0/0","571,0","0","571","0/1","238,203","0.4603","441",null,"chr1:32684064:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4467"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","TMEM109","chr11:60920917","TMEM109(S90*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May mediate cellular response to DNA damage by protecting against ultraviolet C-induced cell death (PubMed:23542032). Can form voltage-gated calcium and potassium channels in vitro (By similarity). {ECO:0000250|UniProtKB:O77751, ECO:0000269|PubMed:23542032}.; ",{"$nulls":4},"p.Ser90*","c.269C>A","HIGH","90/243",3,{"$nulls":5},"5","733","705","508","492","669","613","0","0","0","0.3263",{"$nulls":5},"(TMEM109|ENSG00000110108|1|1.00)","(TMEM109|ENSG00000110108|1|1.00)",{"$nulls":13},"6.70963",null,null,"1",{"$nulls":3},"0.35",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","678,0","0","678","0/1","437,212","0.3267","649",null,"chr11:60920917:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3191"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","TMEM109","chr11:60920917","TMEM109(S90*)",{"$nulls":6},255,"PASS","Loss Of Function",null,-1,null,"FUNCTION: May mediate cellular response to DNA damage by protecting against ultraviolet C-induced cell death (PubMed:23542032). Can form voltage-gated calcium and potassium channels in vitro (By similarity). {ECO:0000250|UniProtKB:O77751, ECO:0000269|PubMed:23542032}.; ",{"$nulls":4},"p.Ser90*","c.269C>A","HIGH","90/243",3,{"$nulls":5},"5","733","939","508","653","675","836","0","0","0","0.2763",{"$nulls":5},"(TMEM109|ENSG00000110108|1|1.00)","(TMEM109|ENSG00000110108|1|1.00)",{"$nulls":13},"6.70963",null,null,"1",{"$nulls":3},"0.35",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","688,0","0","688","0/1","648,249","0.2776","897",null,"chr11:60920917:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2634"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","TMEM150C","chr4:82502777","TMEM150C(P62L)",{"$nulls":6},255,"PASS","Missense",null,-1,null,"FUNCTION: Component of a mechanosensitive cation channel. Confers mechanically activated (MA) currents with slow inactivation kinetics. May contribute to proprioception. {ECO:0000250|UniProtKB:Q8C8S3}.; ",{"$nulls":4},"p.Pro62Leu","c.185C>T","MODERATE","62/249",5,1,{"$nulls":4},"3","373","329","261","229",null,null,"0","0",{"$nulls":22},"4.253576","0.88","2.78;2.78;.;.","1","-7.13;-7.13;-7.41;-9.27","1.0;1.0;.;.","0.001;0.001;0.001;0.0","0.594;0.594;0.575;.",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","361,0","0","361","0/1","284,37","0.1153","321",null,"chr4:82502777:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1004"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","TMEM200A","chr6:130440750","TMEM200A(G110S)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense","rs760128313",1.5000000000000002E-5,{"$nulls":6},"p.Gly110Ser","c.328G>A","MODERATE","110/491",3,{"$nulls":5},"5","384","210","305","166","319","188","0","0","0","0.6064",{"$nulls":20},"1.718758",null,"0.915","0.999987","-2.83;.;-2.83;-2.83","0.401","0.074;.;0.074;0.074","0.097;0.099;0.1;0.102",{"$nulls":3},"ExAC_NFE_AF",1.5000000000000002E-5,{"$nulls":7},"0/0","378,0","0","378","0/1","82,123","0.6","205",null,"chr6:130440750:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.6024"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","TMEM246","chr9:101476324","TMEM246(P257A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro257Ala","c.769C>G","MODERATE","257/403",3,{"$nulls":5},"5","292","240","240","192","256","206","0","0","0","0.4369",{"$nulls":20},"3.676716",null,"2.2","1","-2.27","0.998","0.19","0.512;0.513;0.513",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","292,0","0","292","0/1","130,104","0.4444","234",null,"chr9:101476324:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4427"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","TMEM246","chr9:101476324","TMEM246(P257A)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Pro257Ala","c.769C>G","MODERATE","257/403",3,{"$nulls":5},"5","292","329","240","262","255","290","0","0","0","0.3034",{"$nulls":20},"3.676716",null,"2.2","1","-2.27","0.998","0.19","0.512;0.513;0.513",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","292,0","0","292","0/1","225,96","0.2991","321",null,"chr9:101476324:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3282"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","TNFRSF4","chr1:1212025","TNFRSF4(A184G)",null,null,"topological domain (Extracellular )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Immunodeficiency 16 (IMD16) [MIM:615593]: An autosomal recessive primary immunodeficiency associated with classic Kaposi sarcoma of childhood and poor T-cell recall immune responses due to complete functional OX40 deficiency. {ECO:0000269|PubMed:23897980}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor for TNFSF4/OX40L/GP34. Is a costimulatory molecule implicated in long-term T-cell immunity. {ECO:0000269|PubMed:7704935}.; ",{"$nulls":4},"p.Ala184Gly","c.551C>G","MODERATE","184/277",5,{"$nulls":5},"4","240","348",null,null,"196","271","0","0","0","0.0517",{"$nulls":20},"1.461438","0.07","2.48","1","-0.27","0.808","0.269","0.231",{"$nulls":3},"Unknown",-1,"AR","Immunodeficiency 16","Allergy/Immunology/Infectious",{"$nulls":3},"C3810053","0/0","232,0","0","232","0/1","321,17","0.0503","338",null,"chr1:1212025:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","TP53","chr17:7673802","TP53(R234H)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234C)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234D)), sequence variant (In a sporadic cancer; somatic mutation. TP53(Y234F)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234H)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234N)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234Q)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234S)), strand ",{"$nulls":3},255,"PASS","Missense","rs28934576",9.9403578528827028E-4,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg234His","c.701G>A","MODERATE","234/410",8,1016,{"$nulls":4},"5","222","119","164","88","193","99","0","0","0","0.4848",{"$nulls":20},"3.526684","-7.32;.;.;.;.;.;.;.;-7.32;.;.;-7.32;-7.32;.;.;-7.32;.;.;-7.32",".;.;.;.;.;.;.;.;2.08;.;2.08;2.08;2.08;.;.;2.08;.;.;.","1","-4.61;.;.;.;.;.;.;.;-4.78;.;.;-4.61;-4.61;.;.;-4.78;.;.;-4.31",".;.;.;.;.;.;.;.;0.831;.;0.631;1.0;0.631;.;.;0.831;.;.;.","0.007;.;.;.;.;.;.;.;0.007;.;.;0.008;0.007;.;.;0.007;.;.;0.011","0.954;0.911;0.928;0.934;0.881;0.936;0.919;0.956;0.963;0.956;0.949;0.955;0.949;0.943;0.876;0.965;0.956;0.94;.",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","218,0","0","218","0/1","61,55","0.4741","116",null,"chr17:7673802:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4773"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","TP53","chr17:7673802","TP53(R234H)",null,null,"DNA-binding region , region of interest (Interaction with CCAR2 ), region of interest (Interaction with HIPK1 ), region of interest (Required for interaction with ZNF385A ), region of interest (Required for interaction with FBXO42 ), region of interest (Interaction with AXIN1 ), sequence variant (In LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234C)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234D)), sequence variant (In a sporadic cancer; somatic mutation. TP53(Y234F)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234H)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234K)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs864622237. TP53(Y234N)), sequence variant (In a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions. TP53(Y234Q)), sequence variant (In sporadic cancers; somatic mutation; dbSNP:rs587780073. TP53(Y234S)), strand ",{"$nulls":3},255,"PASS","Missense","rs28934576",9.9403578528827028E-4,"DISEASE: Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma.; DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Li-Fraumeni syndrome (LFS) [MIM:151623]: An autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers. {ECO:0000269|PubMed:10484981, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:1737852, ECO:0000269|PubMed:1933902, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:2259385, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920, ECO:0000269|PubMed:9452042}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355]: A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. Note=The gene represented in this entry is involved in disease pathogenesis.; DISEASE: Lung cancer (LNCR) [MIM:211980]: A common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Papilloma of choroid plexus (CPP) [MIM:260500]: A benign tumor of neuroectodermal origin that generally occurs in childhood, but has also been reported in adults. Although generally found within the ventricular system, choroid plexus papillomas can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. Patients present with signs and symptoms of increased intracranial pressure including headache, hydrocephalus, papilledema, nausea, vomiting, cranial nerve deficits, gait impairment, and seizures. {ECO:0000269|PubMed:12085209}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Adrenocortical carcinoma (ADCC) [MIM:202300]: A malignant neoplasm of the adrenal cortex and a rare childhood tumor. It occurs with increased frequency in patients with Beckwith- Wiedemann syndrome and Li-Fraumeni syndrome. {ECO:0000269|PubMed:11481490}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Basal cell carcinoma 7 (BCC7) [MIM:614740]: A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter. {ECO:0000269|PubMed:21946351}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; ","FUNCTION: Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; the function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA- Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seems to have an effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis. Regulates the circadian clock by repressing CLOCK-ARNTL/BMAL1- mediated transcriptional activation of PER2 (PubMed:24051492). {ECO:0000269|PubMed:11025664, ECO:0000269|PubMed:12810724, ECO:0000269|PubMed:15186775, ECO:0000269|PubMed:15340061, ECO:0000269|PubMed:17317671, ECO:0000269|PubMed:17349958, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:20673990, ECO:0000269|PubMed:20959462, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:24051492, ECO:0000269|PubMed:9840937}.; ","acmg|gedi|foundationOne|illumina|ion|tcga-gbm|level2","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","[ \"Sertraline\" , \"Thioridazine\"]","p.Arg234His","c.701G>A","MODERATE","234/410",8,1016,{"$nulls":4},"5","222","196","164","145","193","168","0","0","0","0.4643",{"$nulls":20},"3.526684","-7.32;.;.;.;.;.;.;.;-7.32;.;.;-7.32;-7.32;.;.;-7.32;.;.;-7.32",".;.;.;.;.;.;.;.;2.08;.;2.08;2.08;2.08;.;.;2.08;.;.;.","1","-4.61;.;.;.;.;.;.;.;-4.78;.;.;-4.61;-4.61;.;.;-4.78;.;.;-4.31",".;.;.;.;.;.;.;.;0.831;.;0.631;1.0;0.631;.;.;0.831;.;.;.","0.007;.;.;.;.;.;.;.;0.007;.;.;0.008;0.007;.;.;0.007;.;.;0.011","0.954;0.911;0.928;0.934;0.881;0.936;0.919;0.956;0.963;0.956;0.949;0.955;0.949;0.943;0.876;0.965;0.956;0.94;.",{"$nulls":3},"1000Gp3_EUR_AF",9.9403578528827028E-4,"AD","Li-Fraumeni syndrome; Choroid plexus papilloma; Ependymoma, intracranial; Osteogenic sarcoma; Breast cancer, familial; Hepatoblastoma; Non-Hodgkin lymphoma; Adrenocortical carcinoma; Colorectal cancer","Oncologic","COSMIC,dcPGX,kAPOPTOSIS,kCANCER,kCELL_CYCLE,kMAPK,kP53,kWNT,vp53,vp53",null,null,"C0029463| C2750850| C1835398| C1859972| C0205770| C0006142| C0235974| C2239176| C1527249| C4748488| C2931822| C3553606","0/0","218,0","0","218","0/1","98,97","0.4974","195",null,"chr17:7673802:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.469"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","TRPA1","chr8:72063553","TRPA1(P191S)",null,null,"topological domain (Cytoplasmic ), repeat (ANK 4 )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Episodic pain syndrome, familial, 1 (FEPS1) [MIM:615040]: An autosomal dominant neurologic disorder characterized by onset in infancy of episodic debilitating upper body pain triggered by fasting, cold, and physical stress. The period of intense pain is accompanied by breathing difficulties, tachycardia, sweating, generalized pallor, peribuccal cyanosis, and stiffness of the abdominal wall. Affected individuals do not manifest altered pain sensitivity outside the episodes. {ECO:0000269|PubMed:20547126}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Receptor-activated non-selective cation channel involved in detection of pain and possibly also in cold perception and inner ear function (PubMed:25389312, PubMed:25855297). Has a central role in the pain response to endogenous inflammatory mediators and to a diverse array of volatile irritants, such as mustard oil, cinnamaldehyde, garlic and acrolein, an irritant from tears gas and vehicule exhaust fumes (PubMed:25389312, PubMed:20547126). Is also activated by menthol (in vitro)(PubMed:25389312). Acts also as a ionotropic cannabinoid receptor by being activated by delta(9)-tetrahydrocannabinol (THC), the psychoactive component of marijuana (PubMed:25389312). May be a component for the mechanosensitive transduction channel of hair cells in inner ear, thereby participating in the perception of sounds. Probably operated by a phosphatidylinositol second messenger system (By similarity). {ECO:0000250|UniProtKB:Q8BLA8, ECO:0000269|PubMed:20547126, ECO:0000269|PubMed:25389312, ECO:0000269|PubMed:25855297}.; ",{"$nulls":4},"p.Pro191Ser","c.571C>T","MODERATE","191/1119",5,{"$nulls":5},"5","284","310","172","191","265","278","0","0","0","0.1942",{"$nulls":20},"2.041792","0.57;-0.3",".;2.715","1","-3.24;-3.21",".;0.202","0.018",".;0.27",{"$nulls":3},"Unknown",-1,"AD","Episodic pain syndrome, familial","Neurologic",{"$nulls":3},"C3808667","0/0","275,0","0","275","0/1","235,63","0.2114","298",null,"chr8:72063553:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1937"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","UMODL1","chr21:42088435","UMODL1(D249N)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Asp249Asn","c.745G>A","MODERATE","249/1446",5,{"$nulls":5},"5","595","391","415","267","518","345","0","0","0","0.2435",{"$nulls":20},"0.743486","-0.65;-0.64;-0.65;-0.64",".;.;1.04;1.04","1","-1.83;-1.76;-1.78;-1.76",".;0.218;0.473;0.03","0.31;0.421;0.289;0.373","0.222;0.234;0.224;0.219",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","568,0","0","568","0/1","274,94","0.2554","368",null,"chr21:42088435:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2472"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","VAV1","chr19:6843154","VAV1(S667F)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Couples tyrosine kinase signals with the activation of the Rho/Rac GTPases, thus leading to cell differentiation and/or proliferation.; ",{"$nulls":4},"p.Ser667Phe","c.2000C>T","MODERATE","667/845",22,1,{"$nulls":4},"5","443","597","286","381","371","520","0","0","0","0.2481",{"$nulls":20},"4.052431","1.74;-0.05;-0.05;-0.05;-0.94",".;2.95;.;.;.","0.99999;0.999938",".;.;.;.;-4.86",".;0.42;.;0.142;.",".;.;.;.;0.0","0.773;0.722;0.719;0.714;0.718",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","417,0","0","417","0/1","415,142","0.2549","557",null,"chr19:6843154:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2467"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","VAV1","chr19:6843154","VAV1(S667F)",null,null,"helix ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Couples tyrosine kinase signals with the activation of the Rho/Rac GTPases, thus leading to cell differentiation and/or proliferation.; ",{"$nulls":4},"p.Ser667Phe","c.2000C>T","MODERATE","667/845",22,1,{"$nulls":4},"5","443","593","286","381","376","526","0","0","0","0.2414",{"$nulls":20},"4.052431","1.74;-0.05;-0.05;-0.05;-0.94",".;2.95;.;.;.","0.99999;0.999938",".;.;.;.;-4.86",".;0.42;.;0.142;.",".;.;.;.;0.0","0.773;0.722;0.719;0.714;0.718",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","428,0","0","428","0/1","434,140","0.2439","574",null,"chr19:6843154:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2415"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","WAS","chrX:48686814","WAS(A198V)",{"$nulls":6},255,"PASS","Missense","rs200261212",2.6075619295958278E-4,"DISEASE: Wiskott-Aldrich syndrome (WAS) [MIM:301000]: An X-linked recessive immunodeficiency characterized by eczema, thrombocytopenia, recurrent infections, and bloody diarrhea. Death usually occurs before age 10. {ECO:0000269|PubMed:10447259, ECO:0000269|PubMed:11793485, ECO:0000269|PubMed:20574068, ECO:0000269|PubMed:7753869, ECO:0000269|PubMed:8528198, ECO:0000269|PubMed:8528199, ECO:0000269|PubMed:8682510, ECO:0000269|PubMed:9098856, ECO:0000269|PubMed:9126958, ECO:0000269|PubMed:9445409, ECO:0000269|PubMed:9683546, ECO:0000269|PubMed:9713366}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thrombocytopenia 1 (THC1) [MIM:313900]: Thrombocytopenia is defined by a decrease in the number of platelets in circulating blood, resulting in the potential for increased bleeding and decreased ability for clotting. {ECO:0000269|PubMed:10447259, ECO:0000269|PubMed:11167787, ECO:0000269|PubMed:11877312, ECO:0000269|PubMed:7795648, ECO:0000269|PubMed:8528199}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neutropenia, severe congenital, X-linked (XLN) [MIM:300299]: A disorder of hematopoiesis characterized by maturation arrest of granulopoiesis at the level of promyelocytes with peripheral blood absolute neutrophil counts below 0.5 x 10(9)/l and early onset of severe bacterial infections. {ECO:0000269|PubMed:11242115}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Effector protein for Rho-type GTPases that regulates actin filament reorganization via its interaction with the Arp2/3 complex (PubMed:12235133, PubMed:12769847, PubMed:16275905). Important for efficient actin polymerization (PubMed:8625410, PubMed:12235133, PubMed:16275905). Possible regulator of lymphocyte and platelet function (PubMed:9405671). Mediates actin filament reorganization and the formation of actin pedestals upon infection by pathogenic bacteria (PubMed:18650809). In addition to its role in the cytoplasmic cytoskeleton, also promotes actin polymerization in the nucleus, thereby regulating gene transcription and repair of damaged DNA (PubMed:20574068). Promotes homologous recombination (HR) repair in response to DNA damage by promoting nuclear actin polymerization, leading to drive motility of double-strand breaks (DSBs) (PubMed:29925947). {ECO:0000269|PubMed:12235133, ECO:0000269|PubMed:12769847, ECO:0000269|PubMed:16275905, ECO:0000269|PubMed:18650809, ECO:0000269|PubMed:20574068, ECO:0000269|PubMed:29925947, ECO:0000269|PubMed:8625410, ECO:0000269|PubMed:9405671}.; ","gedi|level2",{"$nulls":3},"p.Ala198Val","c.593C>T","MODERATE","198/502",7,2,{"$nulls":4},"5","303","289","216","200","243","236","0","0","0","0.2797",{"$nulls":20},"0.203557","-6.35;-6.54",".;-0.75","0.925146","-1.36;-1.16",".;0.392","0.328;0.292",".;0.02",{"$nulls":3},"ESP6500_AA_AF",2.6075619295958278E-4,"XL","Wiskott-Aldrich syndrome; Thrombocytopenia 1; Neutropenia, severe congenital, X-linked","Allergy/Immunology/Infectious; Dermatologic; Hematologic","COSMIC","The Wiskott-Aldrich syndrome (WAS) family of proteins share similar domain structure, and are involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton.  The presence of a number of different motifs suggests that they are regulated by a number of different stimuli, and interact with multiple proteins.  Recent studies have demonstrated that these proteins, directly or indirectly, associate with the small GTPase, Cdc42, known to regulate formation of actin filaments, and the cytoskeletal organizing complex, Arp2/3. Wiskott-Aldrich syndrome is a rare, inherited, X-linked, recessive disease characterized by immune dysregulation and microthrombocytopenia, and is caused by mutations in the WAS gene. The WAS gene product is a cytoplasmic protein, expressed exclusively in hematopoietic cells, which show signalling and cytoskeletal abnormalities in WAS patients.  A transcript variant arising as a result of alternative promoter usage, and containing a different 5' UTR sequence, has been described, however, its full-length nature is not known. [provided by RefSeq, Jul 2008].  ",null,"C1845987| C0043194| C1839163","0/0","297,0","0","297","0/1","206,71","0.2563","277",null,"chrX:48686814:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.265"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","WAS","chrX:48686814","WAS(A198V)",{"$nulls":6},255,"PASS","Missense","rs200261212",2.6075619295958278E-4,"DISEASE: Wiskott-Aldrich syndrome (WAS) [MIM:301000]: An X-linked recessive immunodeficiency characterized by eczema, thrombocytopenia, recurrent infections, and bloody diarrhea. Death usually occurs before age 10. {ECO:0000269|PubMed:10447259, ECO:0000269|PubMed:11793485, ECO:0000269|PubMed:20574068, ECO:0000269|PubMed:7753869, ECO:0000269|PubMed:8528198, ECO:0000269|PubMed:8528199, ECO:0000269|PubMed:8682510, ECO:0000269|PubMed:9098856, ECO:0000269|PubMed:9126958, ECO:0000269|PubMed:9445409, ECO:0000269|PubMed:9683546, ECO:0000269|PubMed:9713366}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thrombocytopenia 1 (THC1) [MIM:313900]: Thrombocytopenia is defined by a decrease in the number of platelets in circulating blood, resulting in the potential for increased bleeding and decreased ability for clotting. {ECO:0000269|PubMed:10447259, ECO:0000269|PubMed:11167787, ECO:0000269|PubMed:11877312, ECO:0000269|PubMed:7795648, ECO:0000269|PubMed:8528199}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neutropenia, severe congenital, X-linked (XLN) [MIM:300299]: A disorder of hematopoiesis characterized by maturation arrest of granulopoiesis at the level of promyelocytes with peripheral blood absolute neutrophil counts below 0.5 x 10(9)/l and early onset of severe bacterial infections. {ECO:0000269|PubMed:11242115}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ","FUNCTION: Effector protein for Rho-type GTPases that regulates actin filament reorganization via its interaction with the Arp2/3 complex (PubMed:12235133, PubMed:12769847, PubMed:16275905). Important for efficient actin polymerization (PubMed:8625410, PubMed:12235133, PubMed:16275905). Possible regulator of lymphocyte and platelet function (PubMed:9405671). Mediates actin filament reorganization and the formation of actin pedestals upon infection by pathogenic bacteria (PubMed:18650809). In addition to its role in the cytoplasmic cytoskeleton, also promotes actin polymerization in the nucleus, thereby regulating gene transcription and repair of damaged DNA (PubMed:20574068). Promotes homologous recombination (HR) repair in response to DNA damage by promoting nuclear actin polymerization, leading to drive motility of double-strand breaks (DSBs) (PubMed:29925947). {ECO:0000269|PubMed:12235133, ECO:0000269|PubMed:12769847, ECO:0000269|PubMed:16275905, ECO:0000269|PubMed:18650809, ECO:0000269|PubMed:20574068, ECO:0000269|PubMed:29925947, ECO:0000269|PubMed:8625410, ECO:0000269|PubMed:9405671}.; ","gedi|level2",{"$nulls":3},"p.Ala198Val","c.593C>T","MODERATE","198/502",7,2,{"$nulls":4},"5","303","358","216","253","242","279","0","0","0","0.3262",{"$nulls":20},"0.203557","-6.35;-6.54",".;-0.75","0.925146","-1.36;-1.16",".;0.392","0.328;0.292",".;0.02",{"$nulls":3},"ESP6500_AA_AF",2.6075619295958278E-4,"XL","Wiskott-Aldrich syndrome; Thrombocytopenia 1; Neutropenia, severe congenital, X-linked","Allergy/Immunology/Infectious; Dermatologic; Hematologic","COSMIC","The Wiskott-Aldrich syndrome (WAS) family of proteins share similar domain structure, and are involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton.  The presence of a number of different motifs suggests that they are regulated by a number of different stimuli, and interact with multiple proteins.  Recent studies have demonstrated that these proteins, directly or indirectly, associate with the small GTPase, Cdc42, known to regulate formation of actin filaments, and the cytoskeletal organizing complex, Arp2/3. Wiskott-Aldrich syndrome is a rare, inherited, X-linked, recessive disease characterized by immune dysregulation and microthrombocytopenia, and is caused by mutations in the WAS gene. The WAS gene product is a cytoplasmic protein, expressed exclusively in hematopoietic cells, which show signalling and cytoskeletal abnormalities in WAS patients.  A transcript variant arising as a result of alternative promoter usage, and containing a different 5' UTR sequence, has been described, however, its full-length nature is not known. [provided by RefSeq, Jul 2008].  ",null,"C1845987| C0043194| C1839163","0/0","297,0","0","297","0/1","238,108","0.3121","346",null,"chrX:48686814:C:T",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3202"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","WDFY4","chr10:48877103","WDFY4(F443L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe443Leu","c.1329C>A","MODERATE","443/1270",10,{"$nulls":5},"5","166","176","119","128","142","138","0","0","0","0.3406",{"$nulls":20},"3.876996","0.48","2.84","0.995882;1","-2.29","0.999","0.697","0.387",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","162,0","0","162","0/1","111,58","0.3432","169",null,"chr10:48877103:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3203"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","WDFY4","chr10:48877103","WDFY4(F443L)",{"$nulls":6},255,"PASS","Missense",null,-1,{"$nulls":6},"p.Phe443Leu","c.1329C>A","MODERATE","443/1270",10,{"$nulls":5},"5","166","190","119","141","141","163","0","0","0","0.2147",{"$nulls":20},"3.876996","0.48","2.84","0.995882;1","-2.29","0.999","0.697","0.387",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","160,0","0","160","0/1","147,38","0.2054","185",null,"chr10:48877103:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.227"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","WDR90","chr16:653351","WDR90(T378N)",null,null,"splice variant (In isoform 2 and isoform 4. )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Required for efficient primary cilium formation. {ECO:0000269|PubMed:28781053}.; ",{"$nulls":4},"p.Thr378Asn","c.1133C>A","MODERATE","378/1750",11,{"$nulls":5},"5","342","259","277","207","264","215","0","0","0","0.3349",{"$nulls":20},"2.566767","5.06",".;2.8","0.99484;0.99484;1;1","-2.99",".;0.991","0.044","0.533;0.574",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","326,0","0","326","0/1","161,85","0.3455","246",null,"chr16:653351:C:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3237"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ZC3H10","chr12:56121360","ZC3H10(E266D)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA. {ECO:0000269|PubMed:28431233}.; ",{"$nulls":4},"p.Glu266Asp","c.798G>C","MODERATE","266/434",3,{"$nulls":5},"4","470","385","385","320","363","311","0","0","0","0.373",{"$nulls":20},"1.390475",null,"2.125","0.999784","-0.91","0.65","0.164","0.419",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","464,0","0","464","0/1","251,127","0.336","378",null,"chr12:56121360:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.35"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ZC3H10","chr12:56121360","ZC3H10(E266D)",null,null,"coiled-coil region ",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA. {ECO:0000269|PubMed:28431233}.; ",{"$nulls":4},"p.Glu266Asp","c.798G>C","MODERATE","266/434",3,{"$nulls":5},"4","470","443","385","362","362","352","0","0","0","0.2642",{"$nulls":20},"1.390475",null,"2.125","0.999784","-0.91","0.65","0.164","0.419",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","458,0","0","458","0/1","316,116","0.2685","432",null,"chr12:56121360:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.279"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ZC3H10","chr12:56121636","ZC3H10(L358F)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA. {ECO:0000269|PubMed:28431233}.; ",{"$nulls":4},"p.Leu358Phe","c.1074G>C","MODERATE","358/434",3,{"$nulls":5},"5","337","276","257","220","186","143","0","0","0","0.3706",{"$nulls":20},"2.867956",null,"0.695","0.99979","-0.4","0.906","0.024","0.316",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","288,0","0","288","0/1","166,74","0.3083","240",null,"chr12:56121636:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3091"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ZC3H10","chr12:56121636","ZC3H10(L358F)",null,null,"compositionally biased region (Pro-rich )",{"$nulls":3},255,"PASS","Missense",null,-1,null,"FUNCTION: Specific regulator of miRNA biogenesis. Binds, via the C3H1-type zinc finger domains, to the binding motif 5'-GCAGCGC-3' on microRNA pri-MIR143 and negatively regulates the processing to mature microRNA. {ECO:0000269|PubMed:28431233}.; ",{"$nulls":4},"p.Leu358Phe","c.1074G>C","MODERATE","358/434",3,{"$nulls":5},"5","337","339","257","255","187","198","0","0","0","0.2828",{"$nulls":20},"2.867956",null,"0.695","0.99979","-0.4","0.906","0.024","0.316",{"$nulls":3},"Unknown",-1,{"$nulls":7},"0/0","284,0","0","284","0/1","211,84","0.2847","295",null,"chr12:56121636:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.2667"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ZNF334","chr20:46502345","ZNF334(R355W)",{"$nulls":6},255,"PASS","Missense","rs201701826",0.0002311,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Arg355Trp","c.1063C>T","MODERATE","355/703",4,{"$nulls":5},"4","595","762","467","591","480","641","0","0","0","0.1966",{"$nulls":20},"1.3022529999999999",".;5.4;3.19;5.4;.",".;1.685;.;.;.","1",".;-2.98;-2.8;.;.",".;0.011;.;0.021;.",".;0.001;0.001;.;.","0.07;0.069;0.084;0.097;0.088",{"$nulls":3},"ExAC_EAS_AF",0.0002311,{"$nulls":7},"0/0","576,0","0","576","0/1","597,152","0.2029","749",null,"chr20:46502345:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.203"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ZNF334","chr20:46502345","ZNF334(R355W)",{"$nulls":6},255,"PASS","Missense","rs201701826",0.0002311,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Arg355Trp","c.1063C>T","MODERATE","355/703",4,{"$nulls":5},"4","595","937","467","747","477","728","0","0","0","0.103",{"$nulls":20},"1.3022529999999999",".;5.4;3.19;5.4;.",".;1.685;.;.;.","1",".;-2.98;-2.8;.;.",".;0.011;.;0.021;.",".;0.001;0.001;.;.","0.07;0.069;0.084;0.097;0.088",{"$nulls":3},"ExAC_EAS_AF",0.0002311,{"$nulls":7},"0/0","569,1","0.0018","570","0/1","801,103","0.1139","904",null,"chr20:46502345:G:A",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.1151"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ZNF692","chr1:248856292","ZNF692(D224H)",{"$nulls":6},255,"PASS","Missense","rs760497594",1.5570000000000002E-5,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp224His","c.670G>C","MODERATE","224/524",6,{"$nulls":5},"5","104","130","88","110","72","106","0","0","0","0.4528",{"$nulls":20},"3.608141","3.16;3.14","1.445;.","0.99993;0.999589;0.99993;1;1","-1.03;-1.13","1.0;.","0.045;0.043","0.424;0.417",{"$nulls":3},"ExAC_NFE_AF",1.5570000000000002E-5,{"$nulls":7},"0/0","101,0","0","101","0/1","78,51","0.3953","129",null,"chr1:248856292:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.4182"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ZNF692","chr1:248856292","ZNF692(D224H)",{"$nulls":6},255,"PASS","Missense","rs760497594",1.5570000000000002E-5,null,"FUNCTION: May be involved in transcriptional regulation.; ",{"$nulls":4},"p.Asp224His","c.670G>C","MODERATE","224/524",6,{"$nulls":5},"5","104","110","88","92","73","83","0","0","0","0.4819",{"$nulls":20},"3.608141","3.16;3.14","1.445;.","0.99993;0.999589;0.99993;1;1","-1.03;-1.13","1.0;.","0.045;0.043","0.424;0.417",{"$nulls":3},"ExAC_NFE_AF",1.5570000000000002E-5,{"$nulls":7},"0/0","101,0","0","101","0/1","64,42","0.3962","106",null,"chr1:248856292:C:G",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.3696"]
["12GW","T11","JLPIKTOR_JLPIKTOR_17113012GW","ZSWIM6","chr5:61543957","ZSWIM6(K1096N)",null,null,"sequence variant (In NEDMAGA. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Acromelic frontonasal dysostosis (AFND) [MIM:603671]: A rare variant form of frontonasal dysplasia, an array of abnormalities affecting the eyes, forehead and nose and linked to midfacial dysraphia. The clinical picture is highly variable. Major findings include true ocular hypertelorism, broadening of the nasal root, median facial cleft affecting the nose and/or upper lip and palate, unilateral or bilateral clefting of the alae nasi, lack of formation of the nasal tip, anterior cranium bifidum occultum, a V-shaped or widow's peak frontal hairline. AFND is characterized by the association of frontonasal malformations with various combinations of polydactyly, tibial hypoplasia, epibulbar dermoid, encephalocoele, corpus callosum agenesis and Dandy-Walker malformation. {ECO:0000269|PubMed:25105228}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic features (NEDMAGA) [MIM:617865]: An autosomal dominant neurodevelopmental disorder characterized by infantile-onset global developmental delay, severe to profound intellectual disability, mildly delayed walking with broad-based and unsteady gait, and absence of meaningful language. Patients have features of autism, with repetitive behaviors and poor communication, but usually are socially reactive and have a happy demeanor. More variable neurologic features include mild seizures, spasticity, and peripheral neuropathy. {ECO:0000269|PubMed:29198722}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ",{"$nulls":5},"p.Lys1096Asn","c.3288G>C","MODERATE","1096/1215",14,{"$nulls":5},"4","904","693","712","536","791","597","0","0","0","0.7873",{"$nulls":20},"3.154719","0.72","2.125","0.894831","-3.75","1.0","0.234","0.491",{"$nulls":3},"Unknown",-1,"AD","Acromelic frontonasal dysostosis","Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C1863616| C4693405","0/0","885,0","0","885","0/1","143,533","0.7885","676",null,"chr5:61543957:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T11_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.7873"]
["12GW","T12","JLPIKTOR_JLPIKTOR_17113012GW","ZSWIM6","chr5:61543957","ZSWIM6(K1096N)",null,null,"sequence variant (In NEDMAGA. )",{"$nulls":3},255,"PASS","Missense",null,-1,"DISEASE: Acromelic frontonasal dysostosis (AFND) [MIM:603671]: A rare variant form of frontonasal dysplasia, an array of abnormalities affecting the eyes, forehead and nose and linked to midfacial dysraphia. The clinical picture is highly variable. Major findings include true ocular hypertelorism, broadening of the nasal root, median facial cleft affecting the nose and/or upper lip and palate, unilateral or bilateral clefting of the alae nasi, lack of formation of the nasal tip, anterior cranium bifidum occultum, a V-shaped or widow's peak frontal hairline. AFND is characterized by the association of frontonasal malformations with various combinations of polydactyly, tibial hypoplasia, epibulbar dermoid, encephalocoele, corpus callosum agenesis and Dandy-Walker malformation. {ECO:0000269|PubMed:25105228}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic features (NEDMAGA) [MIM:617865]: An autosomal dominant neurodevelopmental disorder characterized by infantile-onset global developmental delay, severe to profound intellectual disability, mildly delayed walking with broad-based and unsteady gait, and absence of meaningful language. Patients have features of autism, with repetitive behaviors and poor communication, but usually are socially reactive and have a happy demeanor. More variable neurologic features include mild seizures, spasticity, and peripheral neuropathy. {ECO:0000269|PubMed:29198722}. Note=The disease is caused by mutations affecting the gene represented in this entry.; ",{"$nulls":5},"p.Lys1096Asn","c.3288G>C","MODERATE","1096/1215",14,{"$nulls":5},"4","904","927","712","687","789","804","0","0","0","0.6318",{"$nulls":20},"3.154719","0.72","2.125","0.894831","-3.75","1.0","0.234","0.491",{"$nulls":3},"Unknown",-1,"AD","Acromelic frontonasal dysostosis","Craniofacial; Musculoskeletal; Neurologic",{"$nulls":3},"C1863616| C4693405","0/0","886,0","0","886","0/1","332,578","0.6352","910",null,"chr5:61543957:G:C",0,0,"SNV","JLPIKTOR.JLPIKTOR_17113012GW","somatic","somatic","JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","/labs/ngd-data/VCF38/JLPIKTOR/JLPIKTOR_17113012GW/somatic/JLPIKTOR_17113012GW_1_PB_WBC_C9_A3S7X-JLPIKTOR_17113012GW_1_BE_Whole_T12_A3S7X.bwa.merged.db.snpeff.can.vcf.gz","mergedVcfFile","PASS","tumor","significant","0.623"]