A. patient 1,,,,,,,,,,,,,,,
Chr,Start,End,Ref,Alt,Gene.refGene,ExonicFunc.refGene,,SIFT_pred,Polyphen2_HDIV_pred,Polyphen2_HVAR_pred,MutationTaster_pred,ExAC_ALL,gnomAD_genome_ALL,gnomAD_exome_ALL,
chr2,172691260,172691260,C,T,SLC25A12,nonsynonymous SNV,NM_003705:exon7:c.G728A:p.R243K,T,B,B,D,0.0112,0.009,0.011,-0.119880343
chr3,195509957,195509957,A,T,MUC4,nonsynonymous SNV,NM_018406:exon2:c.T8494A:p.S2832T,.,P,B,N,.,.,.,0.032065979
chr3,195509977,195509977,A,G,MUC4,nonsynonymous SNV,NM_018406:exon2:c.T8474C:p.V2825A,.,.,.,N,0.0004,0.0005,0.0000888,0.032065979
chr3,195509986,195509986,G,A,MUC4,nonsynonymous SNV,NM_018406:exon2:c.C8465T:p.A2822V,.,P,B,N,0.0000975,0.0000934,0.0000406,0.032065979
chr11,119213319,119213319,C,A,MFRP,nonsynonymous SNV,NM_031433:exon11:c.G1374T:p.L458F,.,P,B,N,0.0085,0.0067,0.0082,0.159646502
chr19,17397501,17397501,T,G,ANKLE1,nonsynonymous SNV,NM_001278444:exon8:c.T1933G:p.L645V,.,.,.,N,.,.,.,0.006537759
chr19,55316329,55316329,A,G,KIR2DL4,nonsynonymous SNV,NM_001080770:exon3:c.A158G:p.Y53C,T,D,P,N,.,.,.,-0.029584426
chrX,11682884,11682884,G,T,ARHGAP6,nonsynonymous SNV,NM_006125:exon1:c.C65A:p.A22D,D,P,P,N,0,.,0.00000675,-0.101149196
chrX,39932750,39932750,C,T,BCOR,nonsynonymous SNV,NM_001123383:exon4:c.G1849A:p.A617T,T,B,B,N,0.0000228,.,0.0000168,0.027967388
chrX,49346292,49346292,C,G,GAGE12C;GAGE12D;GAGE12E;GAGE12H,nonsynonymous SNV,NM_001098408:exon3:c.C121G:p.P41A,D,D,D,N,0.0034,0.0021,0.0015,0
chrX,65423248,65423248,C,A,HEPH,nonsynonymous SNV,NM_001282141:exon10:c.C1553A:p.A518E,T,B,B,N,0.0000115,.,0.0000112,-0.099353562
chrX,70824307,70824307,G,T,GCNA,stopgain,NM_052957:exon8:c.G1180T:p.E394X,T,.,.,A,.,.,.,0.851073252
chrX,153693126,153693126,C,T,PLXNA3,nonsynonymous SNV,NM_017514:exon10:c.C1958T:p.P653L,D,B,B,D,0.01,0.0066,0.005,-0.064784641
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B. patient 2,,,,,,,,,,,,,,,
Chr,Start,End,Ref,Alt,Gene name,Function,AAChange.information,SIFT,Polyphen2_HDI,Polyphen2_HVAR,MutationTaster,ExAC,gnomAD_exome,gnomAD_genome,r-testis
chr13,103383339,103383339,T,C,CCDC168,nonsynonymous ,NM_001146197:exon4:c.A19708G:p.R6570G,.,D,P,N,0.00005058,0.0003,0.00009692,0.999982946
chr15,72954605,72954605,C,G,GOLGA6B,nonsynonymous ,NM_018652:exon11:c.C860G:p.S287C,D,D,D,N,.,.,.,0.99943537
chr20,32255934,32255934,A,T,ACTL10,nonsynonymous ,NM_001024675:exon1:c.A631T:p.T211S,D,P,B,D,0.0005,0.0004,0.00009697,0.999009731
chr6,160231077,160231077,T,C,PNLDC1,nonsynonymous ,NM_001271862:exon10:c.T803C:p.M268T,T,D,D,D,0.000008237,.,.,0.970166909
chrX,70823781,70823781,AG,GC,GCNA,nonsynonymous ,NM_052957:exon8:c.653_654GC:p.K218S,[T],[B],,[PN],,< 0.00005,< 0.00005,0.851073252
chr16,4546157,4546157,G,T,HMOX2,nonsynonymous ,NM_001286267:exon2:c.G11T:p.R4L,.,.,.,N,.,.,0.0027,0.781863553
chr5,891394,891394,C,T,BRD9,nonsynonymous ,NM_001009877:exon3:c.G122A:p.R41K,T,B,B,D,0.001,0.0006,0.0003,0.346689198
chrX,36091379,36091379,A,C,CFAP47,nonsynonymous ,NM_001304548:exon29:c.A4589C:p.H1530P,T,P,B,N,0.0098,0.0098,0.0087,0.280625168
chr2,136561517,136561517,T,C,LCT,nonsynonymous ,NM_002299:exon11:c.A4646G:p.Y1549C,T,B,B,N,0.001,0.0008,0.0003,0.23960983
chr12,8926292,8926292,C,T,RIMKLB,nonsynonymous ,NM_001297776:exon6:c.C1073T:p.T358M,D,D,B,D,0.0018,0.0016,0.0023,0.177548148
chr8,48691068,48691068,G,A,PRKDC,unknown,UNKNOWN,.,.,.,.,0.0055,0.0054,0.0074,0.110667309
chrX,106143987,106143987,C,A,RIPPLY1,stopgain,NM_001171706:exon2:c.G307T:p.E103X,.,.,.,N,.,.,.,0.096509993
chr6,159006373,159006373,A,C,TMEM181,nonsynonymous ,NM_020823:exon5:c.A708C:p.K236N,T,P,B,D,0.006,0.0061,0.0046,0.085990253
chr12,9840648,9840648,C,T,CLEC2D,nonsynonymous ,NM_001197317:exon2:c.C212T:p.A71V,D,D,D,N,.,.,.,0.064229557
chrX,39935760,39935760,C,T,BCOR,nonsynonymous ,NM_001123383:exon3:c.G112A:p.A38T,D,D,P,N,0.00002289,0.00002237,.,0.027967388
chr4,9213757,9213757,G,C,USP17L10,nonsynonymous ,NM_001256852:exon1:c.G1375C:p.V459L,T,.,.,N,0.0003,0.0008,0,0
chr8,7830422,7830422,C,A,USP17L8,nonsynonymous ,NM_001256872:exon1:c.G354T:p.Q118H,.,.,.,.,.,0.0002,.,0
chr1,95609573,95609573,A,C,TMEM56,nonsynonymous,NM_001199679:exon2:c.A116C:p.N39T,T,B,B,.,.,.,.,-0.000471716
chr12,18473932,18473932,C,G,PIK3C2G,nonsynonymous ,NM_001288772:exon7:c.C1174G:p.L392V,D,D,P,D,0.0021,0.0014,0.0004,-0.007681969
chr20,40033340,40033340,C,T,CHD6,nonsynonymous ,NM_032221:exon37:c.G8041A:p.G2681S,T,B,B,N,0.000008862,0.000008636,.,-0.009252134
chr17,72851005,72851005,C,T,GRIN2C,nonsynonymous ,NM_000835:exon2:c.G227A:p.S76N,T,P,B,N,.,.,.,-0.014111639
chr20,20349357,20349357,C,T,INSM1,nonsynonymous ,NM_002196:exon1:c.C446T:p.A149V,D,B,B,N,.,.,.,-0.027001455
chr17,73636303,73636303,C,A,SMIM5,nonsynonymous ,NM_001162995:exon2:c.C22A:p.Q8K,T,B,B,D,0.0019,0.0009,0.0045,-0.029410754
chr2,241835292,241835292,G,C,C2orf54,nonsynonymous ,NM_001085437:exon1:c.C123G:p.N41K,D,P,B,N,.,0.000005057,0.00006465,-0.034161609
chrX,152139014,152139014,G,A,ZNF185,nonsynonymous ,NM_001178115:exon8:c.G913A:p.D305N,T,P,B,D,0.0000115,0.00006732,0.00009498,-0.039225132
chr20,23028638,23028638,C,G,THBD,nonsynonymous ,NM_000361:exon1:c.G1504C:p.G502R,T,P,B,N,0.0023,0.0014,0.0057,-0.050653074
chr8,82357149,82357149,A,G,PMP2,nonsynonymous ,NM_002677:exon2:c.T149C:p.I50T,D,P,P,D,0.0068,0.007,0.0056,-0.065184528
chr17,74475241,74475241,G,A,RHBDF2,nonsynonymous ,NM_001005498:exon4:c.C391T:p.R131C,D,D,D,N,0.00008466,0.00009128,.,-0.093488002
chr13,99534228,99534228,C,A,DOCK9,nonsynonymous ,NM_001130049:exon24:c.G2596T:p.A866S,T,B,B,D,.,.,.,-0.096032059
chr13,74420351,74420351,C,T,KLF12,nonsynonymous ,NM_007249:exon4:c.G283A:p.A95T,T,B,B,D,0.0005,0.0004,.,-0.100848167
chr20,39977742,39977742,G,A,LPIN3,nonsynonymous ,NM_001301860:exon5:c.G571A:p.E191K,T,B,B,D,0.0018,0.0017,0.005,-0.109598656
chrY,16936082,16936082,G,A,NLGN4Y,nonsynonymous ,NM_001206850:exon4:c.G136A:p.G46S,D,D,D,.,.,.,.,-0.119520511
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Supplementary Table 3: Population frequencies and In-silico predictions for the effect of the candidate variations in patient 1 (A) and patients 2 (B). ,,,,,,,,,,,,,,,
"A-   Disease causing automate, D- damaging, B- benign, P-polymorphism, N-neutral, PN-probably neutral T- tolerated. The parentheses in (B) for the GCNA variation NM_052957:exon8:c.653_654GC:p.K218S were inserted since both the annovar and the VEP software did not precompiled prediction for the tandem substitution. Therefore, the analyses were done manually compared to the protein sequence. The predictions of beginning effects for this variation in the IDR segments, without known motifs, are probably due to very low conservation of the domain between orthologs (only in primates).",,,,,,,,,,,,,,,
See separate excel file figure. ,,,,,,,,,,,,,,,
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