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["Supplementray Table2: Filtering results from whole exome sequencing for patient II.5 using the 150 genes panel from Table 1"]
[]
["Gene","Variant","Chr","Coordinate","Type","Genotype","Read Depth","Transcript","Consequence","cDNA Position","Protein Position","Amino Acids","Sift","PolyPhen","ENSP","HGVSc","HGVSp","dbSNP ID","Allele Freq","Allele Freq Global Minor","Global Minor Allele","Allele Freq Amr","Allele Freq Eas","Allele Freq Sas","Allele Freq Af","Allele Freq Eur","EVS Freq All","EVS Coverage","EVS Samples","ExAC Freq All","ExAC Freq Afr","ExAC Freq Amr","ExAC Freq Eas","ExAC Freq Sas","ExAC Freq Fin","ExAC Freq Nfe","ExAC Freq Other","ExAC Coverage","ExAC Samples","ClinVar Accession","ClinVar Alleles","ClinVar Significance","ClinVar Disease Name"]
["TSPEAR,TSPEAR-AS1","G>A/A",21,45928766,"snv","hom",39,"NM_144991.2","intron_variant",null,0,{"$nulls":3},"NP_659428.2","NM_144991.2:c.1754+316C>T",null,"rs201339485",0.06,0.06,"A",0.14,0,0,0.07,0.1,0.03,1600,2867,0.05,0,0.16,0,0,0,0.06,0,2800,34306]
["MYO15A","T>C/C",17,18023568,"snv","hom",75,"NM_016239.3","missense_variant",1792,485,"V/A",null,"benign (0.153)","NP_057323.3","NM_016239.3:c.1454T>C","NP_057323.3:p.Val485Ala","rs200532919",0.04,0.04,"C",0,0,0,0,0.2,0.09,4300,6223,0.09,0,0.06,0,0.16,0,0.11,0.34,2500,59452,"RCV000175875.1:RCV000223359.1","C","uncertain significance"]
["STRC","ACCTGCAGCTTCC>A/A",15,43906392,"deletion","hom",53,"NM_153700.2","splice_donor_variant,coding_sequence_variant","2381-?",0,{"$nulls":3},"NP_714544.1","NM_153700.2:c.2303_2313+1delGGAAGCTGCAGG",null,null,0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["STRC","TTGTGTG>T/T",15,43903198,"deletion","hom",145,"NM_153700.2","intron_variant",null,0,{"$nulls":3},"NP_714544.1","NM_153700.2:c.3307-22_3307-17delCACACA",null,null,0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["MITF","C>T/T",3,70005681,"snv","hom",33,"NM_198159.2","missense_variant,splice_region_variant",1176,338,"P/L","tolerated (0.92)","benign (0.169)","NP_937802.1","NM_198159.2:c.1013C>T","NP_937802.1:p.Pro338Leu","rs756923654",0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["COL11A1","CCAT>C/C",1,103471456,"deletion","hom",38,"NM_080629.2","intron_variant",null,0,{"$nulls":3},"NP_542196.2","NM_080629.2:c.1828-12_1828-10delATG",null,"rs112482103;rs34651202;rs71752747",0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"RCV000079905.4:RCV000153075.2:RCV000153076.2","-:CAT:CATCATCAT","benign:uncertain significance"]
["COL4A5","G>G/A","X",107811978,"snv","het",44,"NM_033380.2","intron_variant",null,0,{"$nulls":3},"NP_203699.1","NM_033380.2:c.322-11G>A",null,"rs764068730",0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3900,43863]
["TSPEAR,KRTAP10-10","T>T/C",21,46057625,"snv","het",31,"NM_144991.2","intron_variant",null,0,{"$nulls":3},"NP_659428.2","NM_144991.2:c.83-69736A>G",null,"rs55677560",0,0,null,0,0,0,0,0,0,0,0,0.05,0.16,0,0.03,0.02,0,0.05,0,11900,17869]
["TSPEAR,KRTAP10-2","C>C/T",21,45971162,"snv","het",32,"NM_144991.2","intron_variant",null,0,{"$nulls":3},"NP_659428.2","NM_144991.2:c.303+16507G>A",null,"rs199922020;rs76415521",0,0,null,0,0,0,0,0,0,0,0,1.01,2.34,0.63,0.73,0.29,0.17,1.19,1.8,7200,59226]
["TSPEAR,KRTAP10-2","G>G/A",21,45971109,"snv","het",45,"NM_144991.2","intron_variant",null,0,{"$nulls":3},"NP_659428.2","NM_144991.2:c.303+16560C>T",null,"rs200984587;rs77233671",0,0,null,0,0,0,0,0,0,0,0,0.23,0.51,0.11,0.11,0.03,0.06,0.3,0.34,7300,59182]
["TMC2","T>T/C",20,2517319,"snv","het",41,"NM_080751.2","intron_variant",null,0,{"$nulls":3},"NP_542789.2","NM_080751.2:c.34+18T>C",null,"rs41282318",0.58,0.58,"C",0.14,0.1,2.66,0,0.1,0.24,4400,6484,1.15,0.08,0.35,0,2.12,2.68,0.96,1.75,5200,13779]
["MYH14","G>G/T",19,50747534,"snv","het",74,"NM_001145809.1","missense_variant",1197,384,"G/C","deleterious (0)","probably damaging (1)","NP_001139281.1","NM_001145809.1:c.1150G>T","NP_001139281.1:p.Gly384Cys","rs119103280",0.24,0.24,"T",0.58,0,0.2,0,0.6,0.28,9500,6374,0.29,0.09,0.21,0,0.17,0,0.41,0.79,2800,59997,"RCV000002283.3:RCV000037022.3","T","pathogenic:likely benign","Deafness,_autosomal_dominant_4"]
["ACTG1","G>G/A",17,79478617,"snv","het",42,"NM_001614.3","synonymous_variant",538,133,"Y",null,null,"NP_001605.1","NM_001614.3:c.399C>T","NM_001614.3:c.399C>T(p.=)","rs2230158",2.16,2.16,"A",1.3,4.76,1.74,1.44,1.49,1.42,7400,6503,1.63,1.68,1.45,3.02,1.79,0.6,1.51,2.57,4500,59467,"RCV000116231.3","A","benign"]
["CRYM","G>G/A",16,21273412,"snv","het",33,"NM_001888.3","synonymous_variant",1039,247,"Y",null,null,"NP_001879.1","NM_001888.3:c.741C>T","NM_001888.3:c.741C>T(p.=)","rs34045013",1.28,1.28,"A",0.43,0,0,4.61,0,1.37,8300,6499,0.36,3.97,0.19,0,0,0,0,0,3300,60417,"RCV000150362.1","A","benign"]
["STRC","A>A/G",15,43906636,"snv","het",45,"NM_153700.2","synonymous_variant",2250,724,"V",null,null,"NP_714544.1","NM_153700.2:c.2172T>C","NM_153700.2:c.2172T>C(p.=)",null,0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["ESRRB","C>C/A",14,76905782,"snv","het",40,"NM_004452.3","missense_variant",457,29,"A/D","tolerated - low confidence (0.05)","benign (0.008)","NP_004443.3","NM_004452.3:c.86C>A","NP_004443.3:p.Ala29Asp",null,0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["OTOGL","T>T/C",12,80746068,"snv","het",32,"NM_173591.3","splice_region_variant,intron_variant",null,0,{"$nulls":3},"NP_775862.3","NM_173591.3:c.5239-7T>C",null,"rs79120261",1.12,1.12,"C",1.44,0,1.02,0.38,3.08,2.47,6700,5891,2.15,0.61,1.32,0,0.68,0.76,3.25,1.42,2900,52396,"RCV000216973.1","C","benign"]
["MYO1A","A>A/G",12,57435052,"snv","het",51,"NM_001256041.1","synonymous_variant",1473,395,"F",null,null,"NP_001242970.1","NM_001256041.1:c.1185T>C","NM_001256041.1:c.1185T>C(p.=)","rs17546153",1.7,1.7,"G",2.02,0,1.94,0.23,4.87,3.37,9800,6503,3.59,0.59,2.3,0.01,2.84,3.55,4.93,3.86,4000,60668,"RCV000038469.2","G","benign"]
["MYO7A","C>C/T",11,76924985,"snv","het",83,"NM_000260.3","synonymous_variant",6791,2173,"N",null,null,"NP_000251.3","NM_000260.3:c.6519C>T","NM_000260.3:c.6519C>T(p.=)","rs111033230",0.84,0.84,"T",0.29,0,1.12,1.36,1.09,1.36,13900,6354,1.14,1.04,0.62,0,0.98,0.5,1.5,1.11,5000,60374,"RCV000036237.2:RCV000127064.1","T","benign"]
["MYO7A","C>C/T",11,76916589,"snv","het",61,"NM_000260.3","stop_gained",5835,1855,"Q/*",null,null,"NP_000251.3","NM_000260.3:c.5563C>T","NP_000251.3:p.Gln1855Ter",null,0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["CDH23","C>C/T",10,73377094,"snv","het",54,"NM_022124.5","synonymous_variant",1468,360,"L",null,null,"NP_071407.4","NM_022124.5:c.1078C>T","NM_022124.5:c.1078C>T(p.=)","rs185917383",0.38,0.38,"T",0.14,0,1.84,0,0,0.07,7600,6477,0.27,0.01,0.04,0,1.5,0,0.1,0.45,2500,60294,"RCV000039094.3","T","benign"]
["PCDH15","G>G/T",10,55617042,"snv","het",26,"NM_001142763.1","intron_variant",null,0,{"$nulls":3},"NP_001136235.1","NM_001142763.1:c.3733-19C>A",null,"rs75248212",1.9,1.9,"T",0.86,0.4,4.09,1.66,2.29,2.27,5000,6501,2.33,1.52,1.86,1.19,3.9,0.61,2.45,3.21,3000,59760,"RCV000039731.3","T","benign"]
["SLC26A5","G>G/A",7,103020939,"snv","het",69,"NM_198999.2","synonymous_variant",1834,524,"D",null,null,"NP_945350.1","NM_198999.2:c.1572C>T","NM_198999.2:c.1572C>T(p.=)","rs191358470",0.22,0.22,"A",0,1.09,0,0,0,0,0,0,0.08,0.01,0.01,1.06,0,0,0,0.11,3700,60632,"RCV000155847.1","A","likely benign"]
["EYA4","A>A/G",6,133782321,"snv","het",120,"NM_004100.4","splice_region_variant,intron_variant",null,0,{"$nulls":3},"NP_004091.3","NM_004100.4:c.437+3A>G",null,"rs778942584",0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11,4900,60607]
["FAM65B","A>A/G",6,24825536,"snv","het",50,"NM_014722.2","missense_variant",3025,950,"L/S","deleterious (0)","probably damaging (1)","NP_055537.2","NM_014722.2:c.2849T>C","NP_055537.2:p.Leu950Ser",null,0,0,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
["FGFR3","G>G/T",4,1807478,"snv","het",38,"NM_001163213.1","splice_region_variant,synonymous_variant",1909,551,"G",null,null,"NP_001156685.1","NM_001163213.1:c.1653G>T","NM_001163213.1:c.1653G>T(p.=)","rs3135897",1.98,1.98,"T",1.3,0,0.31,4.39,2.88,2.74,2600,6490,2.17,3.89,0.89,0,1.03,4.26,2.5,2.79,3400,57958]
["FGFR3","C>C/T",4,1805568,"snv","het",40,"NM_001163213.1","intron_variant",null,0,{"$nulls":3},"NP_001156685.1","NM_001163213.1:c.1082-489C>T",null,"rs3135885",1.8,1.8,"T",1.44,0.99,0.82,3.78,1.19,1.62,8400,6503,1.14,3.46,1.09,1.78,1.49,0.04,0.71,1.44,2800,60246]
["COL4A4","C>C/T",2,227915847,"snv","het",40,"NM_000092.4","missense_variant",3650,999,"G/E",null,"unknown (0)","NP_000083.3","NM_000092.4:c.2996G>A","NP_000083.3:p.Gly999Glu","rs13027659",0.46,0.46,"T",0.58,0,0,0.23,1.59,1.14,10900,5998,1.17,0.27,0.81,0,0.34,0.83,1.75,1.33,7100,60385]
["ALMS1","A>A/G",2,73677066,"snv","het",59,"NM_015120.4","missense_variant",3520,1137,"T/A",null,"benign (0.217)","NP_055935.4","NM_015120.4:c.3409A>G","NP_055935.4:p.Thr1137Ala","rs201884768",0,0,null,0,0,0,0,0,0,0,0,0.01,0,0,0,0,0,0.01,0,5300,60330]
["BSND","G>G/T",1,55472790,"snv","het",25,"NM_057176.2","missense_variant",636,131,"L/F","deleterious (0.03)","probably damaging (0.916)","NP_476517.1","NM_057176.2:c.393G>T","NP_476517.1:p.Leu131Phe","rs201387711",0.02,0.02,"T",0,0,0,0,0.1,0.02,6400,6503,0.03,0.04,0.03,0,0,0,0.03,0.11,3000,60614]
["COL9A2","A>A/T",1,40770456,"snv","het",12,"NM_001852.3","intron_variant",null,0,{"$nulls":3},"NP_001843.1","NM_001852.3:c.1161+10T>A",null,"rs117563156",2.04,2.04,"T",2.16,1.79,3.07,1.81,1.49,1.52,3800,6033,3.05,1.43,2.15,1.9,3.63,0,3.19,4.17,3300,10090]