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["Table S4. Detailed information of 21 genes with multiple de novo PTVs/Dmis in our Chinese cohort."]
["Chr","Position","Ref","Alt","Gene symbol","Genbank No.","Effect","Nucleotide change","AA. alteration","Patient_ID","cytoBand","avsnp150","gnomAD_exome_ALL","gnomAD_genome_ALL","RVIS (percentile)","pLI (percentile)","Description","Novel gene screening","SFARI_gene-score","SFARI_syndromic","SFARI_number-of-reports","SFARI_number-autism-reports","Recurrent_in_10_NDD_publications","PMID:25363760 (ASD)","PMID:26402605 (ASD)","PMID:27479843 (ID)","PMID:28135719 (UDD)","PMID:28191889 (ASD)","PMID:28263302 (ASD)","PMID:29262854 (ASD,ID,DD,SCZ)","PMID:29346770 (ASD)","PMID:30559488 (ASD,ID,DD)","PMID:31981491 (ASD)"]
["chr2",166243526,"G","A","SCN2A","NM_001040143","nonsynonymous","c.4822G>A","p.G1608R","A617","2q24.3","rs796053154","-","-","-2.506 (1.1%)","0.999999992 (0.7243%)","sodium voltage-gated channel alpha subunit 2","Known",1,0,62,33,10,"Y","Y","Y","Y","Y","Y","Y","Y","Y","Y"]
["chr2",166211176,"AA","-","SCN2A","NM_001040143","frameshift","c.3394_3395del","p.K1132Rfs*6","A2938","2q24.3","-","-","-","-2.506 (1.1%)","0.999999992 (0.7243%)","sodium voltage-gated channel alpha subunit 2","Known",1,0,62,33,10,"Y","Y","Y","Y","Y","Y","Y","Y","Y","Y"]
["chr2",166198843,"A","G","SCN2A","NM_001040143","nonsynonymous","c.2426A>G","p.K809R",5884,"2q24.3","-","-","-","-2.506 (1.1%)","0.999999992 (0.7243%)","sodium voltage-gated channel alpha subunit 2","Known",1,0,62,33,10,"Y","Y","Y","Y","Y","Y","Y","Y","Y","Y"]
["chr2",166164398,"T","C","SCN2A","NM_001040143","nonsynonymous","c.427T>C","p.C143R","A3031","2q24.3","-","-","-","-2.506 (1.1%)","0.999999992 (0.7243%)","sodium voltage-gated channel alpha subunit 2","Known",1,0,62,33,10,"Y","Y","Y","Y","Y","Y","Y","Y","Y","Y"]
["chr20",49510877,"AT","-","ADNP","NM_001282532","frameshift","c.373_374del","p.I125fs*0",6666,"20q13.13","-","-","-","-1.543 (3.7%)","0.9989041 (5.9753%)","activity-dependent neuroprotector homeobox","Known",1,0,39,23,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr20",49510709,"CTAA","-","ADNP","NM_001282532","frameshift","c.539_542del","p.V180Gfs*16",9246,"20q13.13","rs1057518345","-","-","-1.543 (3.7%)","0.9989041 (5.9753%)","activity-dependent neuroprotector homeobox","Known",1,0,39,23,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr6",33406570,"T","C","SYNGAP1","NM_001130066","nonsynonymous","c.1550T>C","p.L517P","s3576","6p21.32","-","-","-","-2.295 (1.4%)","0.99999845 (1.7942%)","synaptic Ras GTPase activating protein 1","Known",1,0,54,17,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr6",33400537,"A","-","SYNGAP1","NM_001130066","frameshift","c.463delA","p.S155Afs*18",7498,"6p21.32","-","-","-","-2.295 (1.4%)","0.99999845 (1.7942%)","synaptic Ras GTPase activating protein 1","Known",1,0,54,17,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr12",13724844,"C","T","GRIN2B","NM_000834","nonsynonymous","c.2065G>A","p.G689S",7072,"12p13.1","rs869312868","-","-","-2.4767 (1.1%)","0.999994896 (2.1948%)","glutamate ionotropic receptor NMDA type subunit 2B","Known",1,0,53,21,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr12",13724844,"C","T","GRIN2B","NM_000834","nonsynonymous","c.2065G>A","p.G689S","s3588","12p13.1","rs869312868","-","-","-2.4767 (1.1%)","0.999994896 (2.1948%)","glutamate ionotropic receptor NMDA type subunit 2B","Known",1,0,53,21,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr12",13724812,"ATAGTTATTGCGA","-","GRIN2B","NM_000834","frameshift","c.2085_2097del","p.I695Mfs*14","s5162","12p13.1","-","-","-","-2.4767 (1.1%)","0.999994896 (2.1948%)","glutamate ionotropic receptor NMDA type subunit 2B","Known",1,0,53,21,9,"Y","Y","-","Y","Y","Y","Y","Y","Y","Y"]
["chr1",155451241,"T","A","ASH1L","NM_018489","stopgain","c.1420A>T","p.K474X","A2758","1q22","-","-","-","-3.885 (0.3%)","1 (0.1591%)","ash1 (absent, small, or homeotic)-like (Drosophila)","Known",1,0,15,10,8,"Y","Y","-","-","Y","Y","Y","Y","Y","Y"]
["chr1",155451211,"G","A","ASH1L","NM_018489","stopgain","c.1450C>T","p.R484X","A2092","1q22","-","-","-","-3.885 (0.3%)","1 (0.1591%)","ash1 (absent, small, or homeotic)-like (Drosophila)","Known",1,0,15,10,8,"Y","Y","-","-","Y","Y","Y","Y","Y","Y"]
["chr3",41275679,"CA","-","CTNNB1","NM_001098209","frameshift","c.1574_1575del","p.P526Ffs*2","A1957","3p22.1","-","-","-","-1.073 (8.1%)","0.99981275 (4.1975%)","catenin beta 1","Known",1,0,21,6,7,"-","-","Y","Y","Y","-","Y","Y","Y","Y"]
["chr3",41267184,"-","A","CTNNB1","NM_001098209","frameshift","c.769dupA","p.T257Nfs*13","A2434","3p22.1","-","-","-","-1.073 (8.1%)","0.99981275 (4.1975%)","catenin beta 1","Known",1,0,21,6,7,"-","-","Y","Y","Y","-","Y","Y","Y","Y"]
["chr3",41266561,"ACTA","-","CTNNB1","NM_001098209","frameshift","c.358_361del","p.T120Mfs*11","s3224","3p22.1","-","-","-","-1.073 (8.1%)","0.99981275 (4.1975%)","catenin beta 1","Known",1,0,21,6,7,"-","-","Y","Y","Y","-","Y","Y","Y","Y"]
["chr2",60773343,"G","A","BCL11A","NM_018014","stopgain","c.148C>T","p.Q50X","A3343","2p16.1","-","-","-","-1.670 (3.1%)","0.828999685 (20.6255%)","B-cell CLL/lymphoma 11A","Known",1,0,16,7,7,"Y","Y","-","Y","-","-","Y","Y","Y","Y"]
["chr2",60688516,"C","-","BCL11A","NM_018014","frameshift","c.1531delG","p.V511Wfs*6","A3333","2p16.1","-","-","-","-1.670 (3.1%)","0.828999685 (20.6255%)","B-cell CLL/lymphoma 11A","Known",1,0,16,7,7,"Y","Y","-","Y","-","-","Y","Y","Y","Y"]
["chr12",116446221,"CTCT","-","MED13L","NM_015335","frameshift","c.1994_1997del","p.E665Afs*7","A2719","12q24.21","-","-","-","-1.607 (3.3%)","0.999999999 (0.5706%)","mediator complex subunit 13 like","Known",1,0,32,14,6,"-","-","-","Y","Y","-","Y","Y","Y","Y"]
["chr12",116428913,"C","-","MED13L","NM_015335","frameshift","c.3846delG","p.R1283Gfs*16",9284,"12q24.21","-","-","-","-1.607 (3.3%)","0.999999999 (0.5706%)","mediator complex subunit 13 like","Known",1,0,32,14,6,"-","-","-","Y","Y","-","Y","Y","Y","Y"]
["chr12",116408546,"G","A","MED13L","NM_015335","stopgain","c.5920C>T","p.R1974X",7774,"12q24.21","-","-","-","-1.607 (3.3%)","0.999999999 (0.5706%)","mediator complex subunit 13 like","Known",1,0,32,14,6,"-","-","-","Y","Y","-","Y","Y","Y","Y"]
["chr22",51159932,"-","G","SHANK3","NM_033517","frameshift","c.3630dupG","p.A1213Gfs*68",9338,"22q13.33","rs797044936",{"v":6.38e-05,"d":"6.38E-05"},"-","-","0.99983962 (4.1317%)","SH3 and multiple ankyrin repeat domains 3","Known",1,0,81,42,5,"-","Y","-","-","-","Y","Y","-","Y","Y"]
["chr22",51153476,"G","A","SHANK3","NM_033517","splicing","c.2223+1G>A","NA","A3040","22q13.33","-",{"v":6.32e-06,"d":"6.32E-06"},"-","-","0.99983962 (4.1317%)","SH3 and multiple ankyrin repeat domains 3","Known",1,0,81,42,5,"-","Y","-","-","-","Y","Y","-","Y","Y"]
["chrX",153296882,"G","A","MECP2","NM_001110792","nonsynonymous","c.433C>T","p.R145C",6687,"Xq28","rs28934904","-","-","-0.320 (30.3%)","0.698089048 (24.6200%)","methyl-CpG binding protein 2","Known",1,0,81,24,4,"-","-","-","Y","Y","Y","-","-","Y","-"]
["chrX",153296882,"G","A","MECP2","NM_001110792","nonsynonymous","c.433C>T","p.R145C","A3010","Xq28","rs28934904","-","-","-0.320 (30.3%)","0.698089048 (24.6200%)","methyl-CpG binding protein 2","Known",1,0,81,24,4,"-","-","-","Y","Y","Y","-","-","Y","-"]
["chrX",153296516,"G","A","MECP2","NM_001110792","stopgain","c.799C>T","p.R267X","A2534","Xq28","rs61749721","-","-","-0.320 (30.3%)","0.698089048 (24.6200%)","methyl-CpG binding protein 2","Known",1,0,81,24,4,"-","-","-","Y","Y","Y","-","-","Y","-"]
["chrX",153296363,"G","A","MECP2","NM_001110792","nonsynonymous","c.952C>T","p.R318C","s3861","Xq28","rs28935468","-","-","-0.320 (30.3%)","0.698089048 (24.6200%)","methyl-CpG binding protein 2","Known",1,0,81,24,4,"-","-","-","Y","Y","Y","-","-","Y","-"]
["chr2",50765722,"A","C","NRXN1","NM_001330087","nonsynonymous","c.1728T>G","p.S576R",7666,"2p16.3","-","-","-","-1.883 (2.3%)","0.999948738 (3.2209%)","neurexin 1","Known",1,0,82,40,4,"-","Y","-","-","Y","-","Y","-","-","Y"]
["chr2",50723189,"A","T","NRXN1","NM_001330087","nonsynonymous","c.2813T>A","p.I938N",9610,"2p16.3","-",0,"-","-1.883 (2.3%)","0.999948738 (3.2209%)","neurexin 1","Known",1,0,82,40,4,"-","Y","-","-","Y","-","Y","-","-","Y"]
["chr2",200233345,"T","-","SATB2","NM_001172509","frameshift","c.683delA","p.K228Sfs*30","A913","2q33.1","-","-","-","-1.308 (5.4%)","0.999563007 (4.9712%)","SATB homeobox 2","Known",3,1,28,8,3,"-","-","-","Y","-","-","Y","-","Y","-"]
["chr2",200188564,"G","A","SATB2","NM_001172509","stopgain","c.1504C>T","p.Q502X","s4151","2q33.1","-","-","-","-1.308 (5.4%)","0.999563007 (4.9712%)","SATB homeobox 2","Known",3,1,28,8,3,"-","-","-","Y","-","-","Y","-","Y","-"]
["chr20",62103520,"C","T","KCNQ2","NM_004518","splicing","c.296+1G>A","NA","A886","20q13.33","rs118192190","-","-","-1.2497 (6.0%)","0.999356099 (5.3937%)","potassium voltage-gated channel subfamily Q member 2","Known",2,0,24,3,3,"-","-","-","Y","-","-","Y","-","Y","-"]
["chr20",62070955,"G","A","KCNQ2","NM_004518","nonsynonymous","c.923C>T","p.P308L","s4225","20q13.33","-","-","-","-1.2497 (6.0%)","0.999356099 (5.3937%)","potassium voltage-gated channel subfamily Q member 2","Known",2,0,24,3,3,"-","-","-","Y","-","-","Y","-","Y","-"]
["chr20",62065250,"A","C","KCNQ2","NM_004518","nonsynonymous","c.1030T>G","p.W344G",9851,"20q13.33","-","-","-","-1.2497 (6.0%)","0.999356099 (5.3937%)","potassium voltage-gated channel subfamily Q member 2","Known",2,0,24,3,3,"-","-","-","Y","-","-","Y","-","Y","-"]
["chr7",140501302,"T","C","BRAF","NM_004333","nonsynonymous","c.770A>G","p.Q257R",6129,"7q34","rs180177035","-","-","-0.965 (9.6%)","0.999978196 (2.8258%)","B-Raf proto-oncogene, serine/threonine kinase","Known",1,0,8,1,2,"-","-","-","Y","-","-","-","-","Y","-"]
["chr7",140501302,"T","C","BRAF","NM_004333","nonsynonymous","c.770A>G","p.Q257R","s4098","7q34","rs180177035","-","-","-0.965 (9.6%)","0.999978196 (2.8258%)","B-Raf proto-oncogene, serine/threonine kinase","Known",1,0,8,1,2,"-","-","-","Y","-","-","-","-","Y","-"]
["chr3",135870926,"AG","-","MSL2","NM_001145417","frameshift","c.574_575del","p.L192Vfs*3","A671","3q22.3","-","-","-","-0.718 (15.0%)","0.889663742 (18.1893%)","male-specific lethal 2 homolog (Drosophila)","Novel","NA","NA","NA","NA",0,"-","-","-","-","-","-","-","-","-","-"]
["chr3",135870044,"C","-","MSL2","NM_001145417","frameshift","c.1457delG","p.S486Ifs*11","A592","3q22.3","-","-","-","-0.718 (15.0%)","0.889663742 (18.1893%)","male-specific lethal 2 homolog (Drosophila)","Novel","NA","NA","NA","NA",0,"-","-","-","-","-","-","-","-","-","-"]
["chr6",152671433,"T","G","SYNE1","NM_182961","nonsynonymous","c.11771A>C","p.H3924P",6720,"6q25.2","rs756029164","-","-","-1.102 (7.7%)","3.75E-27 (99.4458%)","spectrin repeat containing, nuclear envelope 1","Known",3,1,16,9,0,"-","-","-","-","-","-","-","-","-","-"]
["chr6",152563496,"T","C","SYNE1","NM_033071","nonsynonymous","c.19559A>G","p.Y6520C","A931","6q25.2","rs759071467",{"v":8.12e-06,"d":"8.12E-06"},{"v":3.23e-05,"d":"3.23E-05"},"-1.102 (7.7%)","3.75E-27 (99.4458%)","spectrin repeat containing, nuclear envelope 1","Known",3,1,16,9,0,"-","-","-","-","-","-","-","-","-","-"]
["chrX",53239925,"T","C","KDM5C","NM_001146702","nonsynonymous","c.1315A>G","p.M439V",8743,"Xp11.22","-","-","-","-2.706 (0.9%)","0.997842569 (7.0178%)","lysine demethylase 5C","Known",2,0,23,4,0,"-","-","-","-","-","-","-","-","-","-"]
["chrX",53228240,"C","A","KDM5C","NM_001146702","nonsynonymous","c.1961G>T","p.C654F","A992","Xp11.22","-","-","-","-2.706 (0.9%)","0.997842569 (7.0178%)","lysine demethylase 5C","Known",2,0,23,4,0,"-","-","-","-","-","-","-","-","-","-"]
["chr22",42575645,"G","A","TCF20","NM_005650","stopgain","c.5719C>T","p.R1907X","s4216","22q13.2","-","-","-","-3.824233709 (0.341514%)","0.999977934(2.8368%)","transcription factor 20 (AR1)","Known",1,0,10,3,5,"-","-","Y","Y","-","-","Y","-","Y","Y"]
["chr22",42605926,"CA","-","TCF20","NM_005650","frameshift deletion","c.5385_5386del","p.C1795Wfs*13","A1299","22q13.2","rs869312678","-","-","-3.824233709 (0.341514%)","0.999977934(2.8368%)","transcription factor 20 (AR1)","Known",1,0,10,3,5,"-","-","Y","Y","-","-","Y","-","Y","Y"]
["chr22",42605906,"-","A","TCF20","NM_005650","frameshift insertion","c.5405dupT","p.S1803Vfs*6","A3484","22q13.2","-","-","-","-3.824233709 (0.341514%)","0.999977934(2.8368%)","transcription factor 20 (AR1)","Known",1,0,10,3,5,"-","-","Y","Y","-","-","Y","-","Y","Y"]
["chr1",153782655,"A","G","GATAD2B","NM_020699","stoploss","c.1780T>C","p.X594Q","s5195","1q21.3","-","-","-","-0.647683512 (16.9194%)","0.998594716(6.3429%)","GATA zinc finger domain containing 2B","Known","-","-","-","-",4,"-","-","Y","Y","-","-","Y","-","Y","-"]
["chr1",153791344,"G","A","GATAD2B","NM_020699","stopgain","c.520C>T","p.R174X",8734,"1q21.3","-","-","-","-0.647683512 (16.9194%)","0.998594716(6.3429%)","GATA zinc finger domain containing 2B","Known","-","-","-","-",4,"-","-","Y","Y","-","-","Y","-","Y","-"]
["chr17",18138409,"A","G","LLGL1","NM_004140","nonsynonymous SNV","c.1067A>G","p.D356G",9271,"17p11.2","-","-","-","-1.695070442 (2.9405%)","0.977463207(12.0988%)","lethal giant larvae homolog 1, scribble cell polarity complex component","Known",1,0,11,4,4,"-","-","Y","-","Y","-","Y","-","Y","-"]
["chr17",18141042,"G","A","LLGL1","NM_004140","nonsynonymous SNV","c.1859G>A","p.G620D","A2833","17p11.2","-","-","-","-1.695070442 (2.9405%)","0.977463207(12.0988%)","lethal giant larvae homolog 1, scribble cell polarity complex component","Known",1,0,11,4,4,"-","-","Y","-","Y","-","Y","-","Y","-"]
["chr1",43396395,"C","T","SLC2A1","NM_006516","nonsynonymous SNV","c.418G>A","p.V140M",5303,"1p34.2","rs1057517822","-","-","-0.915582298 (10.4885%)","0.93980813(15.5556%)","solute carrier family 2 member 1","Known","-","-","-","-",1,"-","-","-","-","-","-","Y","-","-","-"]
["chr1",43393298,"C","T","SLC2A1","NM_006516","nonsynonymous SNV","c.1256G>A","p.G419D","A3210","1p34.2","-","-","-","-0.915582298 (10.4885%)","0.93980813(15.5556%)","solute carrier family 2 member 1","Known","-","-","-","-",1,"-","-","-","-","-","-","Y","-","-","-"]